Load phyloseq data generated from dada2

# Load Phyloseq object generated in HIV_oral_preprocessing.Rmd
# Options include GreenGenes, SILVA, RDP and HitDB
ps1 <- readRDS("~/Dropbox/Research/human_volunteer/results/ps1.RDS")
ps1
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 1590 taxa and 100 samples ]
## sample_data() Sample Data:       [ 100 samples by 119 sample variables ]
## tax_table()   Taxonomy Table:    [ 1590 taxa by 7 taxonomic ranks ]
## phy_tree()    Phylogenetic Tree: [ 1590 tips and 1588 internal nodes ]
# View sample variables & generate basic stats
sample_variables(ps1)
##   [1] "X.SampleID"                  "BarcodeSequence"            
##   [3] "LinkerPrimerSequence"        "sequence_ID"                
##   [5] "miseq_run"                   "plate"                      
##   [7] "well"                        "collaborator"               
##   [9] "tissue"                      "number_seqs_slout"          
##  [11] "sample_surviving_dada2"      "sample_ID"                  
##  [13] "tube_ID"                     "patient_ID"                 
##  [15] "randomization"               "day"                        
##  [17] "randomization_arm"           "Date_assessment"            
##  [19] "Age"                         "Gender"                     
##  [21] "Ethnicity"                   "Asthma"                     
##  [23] "Eczema"                      "Hayfever"                   
##  [25] "Allergies"                   "Def_allergies"              
##  [27] "Other_illness"               "Chronic_medication"         
##  [29] "Def_medication"              "Herbs_OTC"                  
##  [31] "def_Herbs_OTC"               "Alcohol"                    
##  [33] "Alcoholunitsweek"            "Smoking"                    
##  [35] "Drugs"                       "Drugstype"                  
##  [37] "Drugsusage"                  "Weight"                     
##  [39] "Length"                      "BMIcalc"                    
##  [41] "SystolicBP"                  "DiastolicBP"                
##  [43] "Pulse"                       "Respfreq"                   
##  [45] "Physical_exam_abnorm"        "def_phys_abnormalities"     
##  [47] "Lab_abnorm_screen"           "def_abnorm_lab_screen"      
##  [49] "Serum_screen"                "PBMC_screen"                
##  [51] "Feces_screen"                "Date_day_9"                 
##  [53] "New_medication_day_9"        "def_new_med_day_9"          
##  [55] "Course_completed"            "Antibiotic_side_effects"    
##  [57] "Def_abx_side_effects"        "Lab_abnorm_post_antibiotics"
##  [59] "def_abnorm_post_antibiotics" "Date_day_0"                 
##  [61] "Feces_day_0"                 "New_medication_day0"        
##  [63] "Def_new_medication_day_0"    "Vaccination_side_effects"   
##  [65] "Def_vac_side_effects"        "Lab_abnorm_post_vaccination"
##  [67] "def_abnorm_post_vaccination" "Date_day_7"                 
##  [69] "Feces_day_1"                 "Feces_day_2"                
##  [71] "Feces_day_3"                 "Feces_day_4"                
##  [73] "Feces_day_5"                 "Feces_day_6"                
##  [75] "Feces_day_7"                 "Serum_day_7"                
##  [77] "New_medication_day7"         "def_new_med_day7"           
##  [79] "Date_day_14"                 "New_medication_day14"       
##  [81] "def_new_med_day14"           "Serum_day_14"               
##  [83] "PBMC_day_14"                 "Date_day_28"                
##  [85] "New_medication_day28"        "def_new_med_day28"          
##  [87] "Serum_day_28"                "PBMC_day_28"                
##  [89] "Study_complete"              "pre_RV_IgA"                 
##  [91] "d7_RV_IgA"                   "boost_change"               
##  [93] "d7_RV_IgA_boost_fc"          "d7_roto_boost"              
##  [95] "d7_rota_boost_updated"       "d14_RV_IgA"                 
##  [97] "d28_RV_IgA"                  "RV_Ag_shedding_d0"          
##  [99] "RV_Ag_shedding_d1"           "RV_Ag_shedding_d2"          
## [101] "RV_Ag_shedding_d3"           "RV_Ag_shedding_d4"          
## [103] "RV_Ag_shedding_d5"           "RV_Ag_shedding_d6"          
## [105] "Shedding"                    "pneumo_IgG_pre"             
## [107] "pneumo_IgG_7"                "pneumo_IgG_14"              
## [109] "pneumo_IgG_28"               "pneumo_IgG_7vPre"           
## [111] "pneumo_IgG_14vPre"           "pneumo_IgG_28vPre"          
## [113] "tetanus_IgG_pre"             "tetanus_IgG_d7"             
## [115] "tetanus_IgG_d14"             "tetanus_IgG_d28"            
## [117] "tetanus_IgG_7vPre"           "tetanus_IgG_14vPre"         
## [119] "tetanus_IgG_28vPre"
sd(sample_sums(ps1))
## [1] 22713.02
get_taxa_unique(ps1, "Phylum")
##  [1] "Bacteroidetes"   "Firmicutes"      "Verrucomicrobia"
##  [4] "Proteobacteria"  "Fusobacteria"    "Synergistetes"  
##  [7] "Actinobacteria"  "Spirochaetes"    "Lentisphaerae"  
## [10] "Euryarchaeota"   "Elusimicrobia"   "Tenericutes"

Differential abundance testing

Likelihood ratio test: Identifying taxa differentially abundant in one or more time points between 1) patients who boosted versus thoses that did not and 2) patients that shed rotavirus in their stool and those that did not

1) Rotavirus Boost or Not

Only testing for categories where there were > 2 samples per variable (boost or Shedding)

BOOST: NARROW SPECTRUM ANTIBIOTICS SAMPLES

# Test for taxa which at one or more time points after time 0 showed a d7-rota-boost-specific effect
# Convert phyloseq object to DeSeq2 table
ds.boost.narrow.LRT <- phyloseq_to_deseq2(ps1.narrow, ~d7_rota_boost_updated + day + d7_rota_boost_updated:day)

# Calculate geometric means prior to estimate size factors
geoMeans.ds.boost.narrow.LRT <- apply(counts(ds.boost.narrow.LRT), 1, gm_mean)
ds.boost.narrow.LRT <- estimateSizeFactors(ds.boost.narrow.LRT, geoMeans = geoMeans.ds.boost.narrow.LRT)

# Run DeSeq2
dds.boost.narrow.LRT <- DESeq(ds.boost.narrow.LRT, test="LRT", reduced = ~d7_rota_boost_updated + day)

# Tabulate results
res.dds.boost.narrow.LRT = results(dds.boost.narrow.LRT)
res.dds.boost.narrow.LRT$symbol <- mcols(dds.boost.narrow.LRT)$symbol
head(res.dds.boost.narrow.LRT[order(res.dds.boost.narrow.LRT$padj), ], 4)
## log2 fold change (MLE): d7 rota boost updatedYes.day7 
## LRT p-value: '~ d7_rota_boost_updated + day + d7_rota_boost_updated:day' vs '~ d7_rota_boost_updated + day' 
## DataFrame with 4 rows and 6 columns
##                                                                                                                                                                                                                                            baseMean
##                                                                                                                                                                                                                                           <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  5327.853
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT  1017.600
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT   842.095
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG  1923.573
##                                                                                                                                                                                                                                           log2FoldChange
##                                                                                                                                                                                                                                                <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT      3.6496383
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT      0.6975514
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT     -0.8585548
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG     -2.0919430
##                                                                                                                                                                                                                                               lfcSE
##                                                                                                                                                                                                                                           <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  6.128345
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT  5.265614
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT  4.588674
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG  5.687215
##                                                                                                                                                                                                                                                 stat
##                                                                                                                                                                                                                                            <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 0.35086417
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.96287868
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.03470478
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG 0.15368236
##                                                                                                                                                                                                                                              pvalue
##                                                                                                                                                                                                                                           <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 0.8390944
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.6178934
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.9827973
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG 0.9260369
##                                                                                                                                                                                                                                                padj
##                                                                                                                                                                                                                                           <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT         1
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT         1
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT         1
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG         1
write.table(res.dds.boost.narrow.LRT, file = "./results/deseq_rotaboost_narrow_LRT.txt", sep = "\t")
mcols(res.dds.boost.narrow.LRT)
## DataFrame with 6 rows and 2 columns
##           type
##    <character>
## 1 intermediate
## 2      results
## 3      results
## 4      results
## 5      results
## 6      results
##                                                                                                     description
##                                                                                                     <character>
## 1                                                                     mean of normalized counts for all samples
## 2                                                         log2 fold change (MLE): d7 rota boost updatedYes.day7
## 3                                                                 standard error: d7 rota boost updatedYes.day7
## 4 LRT statistic: '~ d7_rota_boost_updated + day + d7_rota_boost_updated:day' vs '~ d7_rota_boost_updated + day'
## 5   LRT p-value: '~ d7_rota_boost_updated + day + d7_rota_boost_updated:day' vs '~ d7_rota_boost_updated + day'
## 6                                                                                          BH adjusted p-values
summary(res.dds.boost.narrow.LRT)
## 
## out of 830 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 0, 0% 
## LFC < 0 (down)   : 0, 0% 
## outliers [1]     : 268, 32% 
## low counts [2]   : 133, 16% 
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
# Plot taxa with lowest p-value
fiss.dds.boost.narrow.LRT <- plotCounts(dds.boost.narrow.LRT, which.min(res.dds.boost.narrow.LRT$padj), 
                   intgroup = c("day","d7_rota_boost_updated"), returnData = TRUE)
ggplot(fiss.dds.boost.narrow.LRT,
  aes(x = as.numeric(day), y = count, color = d7_rota_boost_updated, group = d7_rota_boost_updated)) + 
  geom_point() + geom_smooth(se = FALSE, method = "loess") + scale_y_log10()

Interpretation: There are no differentially abundant taxa in any of the randomization arms at any time point between samples that boosted and those that did not boost in narrow spectrum antibiotics treated samples.

2) Shedding or Not: Control samples not analyzed as two few shedders in that group.

Shedding: NARROW SPECTRUM ANTIBIOTICS SAMPLES

# Test for taxa which at one or more time points after time 0 showed a Shedding-specific effect
# Convert phyloseq object to DeSeq2 table
ds.Shedding.narrow.LRT <- phyloseq_to_deseq2(ps1.narrow, ~Shedding + day + Shedding:day)

# Calculate geometric means prior to estimate size factors
geoMeans.ds.Shedding.narrow.LRT <- apply(counts(ds.Shedding.narrow.LRT), 1, gm_mean)
ds.Shedding.narrow.LRT <- estimateSizeFactors(ds.Shedding.narrow.LRT, geoMeans = geoMeans.ds.Shedding.narrow.LRT)

# Run DeSeq2
dds.Shedding.narrow.LRT <- DESeq(ds.Shedding.narrow.LRT, test="LRT", reduced = ~Shedding + day)

# Tabulate results
res.dds.Shedding.narrow.LRT = results(dds.Shedding.narrow.LRT)
res.dds.Shedding.narrow.LRT$symbol <- mcols(dds.Shedding.narrow.LRT)$symbol
head(res.dds.Shedding.narrow.LRT[order(res.dds.Shedding.narrow.LRT$padj), ], 4)
## log2 fold change (MLE): SheddingShedding.day7 
## LRT p-value: '~ Shedding + day + Shedding:day' vs '~ Shedding + day' 
## DataFrame with 4 rows and 6 columns
##                                                                                                                                                                                                                                            baseMean
##                                                                                                                                                                                                                                           <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  5327.853
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT  1017.600
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT   842.095
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  1642.889
##                                                                                                                                                                                                                                           log2FoldChange
##                                                                                                                                                                                                                                                <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT     -0.9416984
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT     -3.2646342
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT     -2.0524161
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT    -30.0000000
##                                                                                                                                                                                                                                               lfcSE
##                                                                                                                                                                                                                                           <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  6.204814
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT  5.451830
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT  4.732296
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  7.953654
##                                                                                                                                                                                                                                                stat
##                                                                                                                                                                                                                                           <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.2560877
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.6442059
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.1880057
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.1519792
##                                                                                                                                                                                                                                              pvalue
##                                                                                                                                                                                                                                           <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 0.1963132
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.7246236
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.9102802
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 0.2068028
##                                                                                                                                                                                                                                                padj
##                                                                                                                                                                                                                                           <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT         1
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT         1
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT         1
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT         1
write.table(res.dds.Shedding.narrow.LRT, file = "./results/deseq_Shedding_narrow_LRT.txt", sep = "\t")
mcols(res.dds.Shedding.narrow.LRT)
## DataFrame with 6 rows and 2 columns
##           type
##    <character>
## 1 intermediate
## 2      results
## 3      results
## 4      results
## 5      results
## 6      results
##                                                              description
##                                                              <character>
## 1                              mean of normalized counts for all samples
## 2                          log2 fold change (MLE): SheddingShedding.day7
## 3                                  standard error: SheddingShedding.day7
## 4 LRT statistic: '~ Shedding + day + Shedding:day' vs '~ Shedding + day'
## 5   LRT p-value: '~ Shedding + day + Shedding:day' vs '~ Shedding + day'
## 6                                                   BH adjusted p-values
summary(res.dds.Shedding.narrow.LRT)
## 
## out of 839 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 0, 0% 
## LFC < 0 (down)   : 0, 0% 
## outliers [1]     : 264, 31% 
## low counts [2]   : 124, 15% 
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
# Plot taxa with lowest p-value
fiss.dds.Shedding.narrow.LRT <- plotCounts(dds.Shedding.narrow.LRT, which.min(res.dds.Shedding.narrow.LRT$padj), 
                   intgroup = c("day","d7_rota_boost_updated"), returnData = TRUE)
ggplot(fiss.dds.Shedding.narrow.LRT,
  aes(x = as.numeric(day), y = count, color = d7_rota_boost_updated, group = d7_rota_boost_updated)) + 
  geom_point() + geom_smooth(se = FALSE, method = "loess") + scale_y_log10()

Interpretation: There are no differentially abundant taxa in any of the randomization arms at any time point between samples that shed rotavirus and those that did not.

Pairwise differential abundance testing

BOOST: Day -9 Narrow Spectrum Antibiotics

sample_data(ps1)$day
##   [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
##  [24] -9  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7
##  [47]  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  0  0  0
##  [70]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [93]  0  0  0  0  0  0  0  0
ps1.d.9.narrow <- subset_samples(ps1.narrow, day == "-9")
sample_data(ps1.d.9.narrow)$day
## [1] -9 -9 -9 -9 -9 -9 -9 -9
## Levels: -9
sample_data(ps1.d.9.narrow)$randomization_arm
## [1] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [3] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [5] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [7] Narrow spectrum antibiotics Narrow spectrum antibiotics
## Levels: Narrow spectrum antibiotics
# Differential Abundance Testing
ds.d.9.narrow <- phyloseq_to_deseq2(ps1.d.9.narrow, ~d7_rota_boost_updated)

geoMeans.ds.d.9.narrow <- apply(counts(ds.d.9.narrow), 1, gm_mean)
ds.d.9.narrow <- estimateSizeFactors(ds.d.9.narrow, geoMeans = geoMeans.ds.d.9.narrow)

dds.d.9.narrow <- DESeq(ds.d.9.narrow, test="Wald", fitType="local", betaPrior = FALSE)

alpha = 0.05

# Tabulate and write results
res.dds.d.9.narrow = results(dds.d.9.narrow, cooksCutoff = FALSE)
sigtab_dds.dds.d.9.narrow = res.dds.d.9.narrow[which(res.dds.d.9.narrow$padj < alpha), ]
sigtab_dds.dds.d.9.narrow = cbind(as(sigtab_dds.dds.d.9.narrow, "data.frame"), as(tax_table(ps1.d.9.narrow)[rownames(sigtab_dds.dds.d.9.narrow), ], "matrix"))
summary(res.dds.d.9.narrow)
## 
## out of 469 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 46, 9.8% 
## LFC < 0 (down)   : 36, 7.7% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 159, 34% 
## (mean count < 4)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
head(sigtab_dds.dds.d.9.narrow)
##                                                                                                                                                                                                                                             baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1766.32988
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG   212.08362
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT    72.68788
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT  195.55351
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT    26.67661
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   48.19724
##                                                                                                                                                                                                                                           log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT      -28.48937
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG        24.78646
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT       -24.11592
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT       24.67326
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT       -22.76311
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT      -23.56139
##                                                                                                                                                                                                                                              lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.383398
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  3.383542
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  3.383988
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.383556
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  3.385049
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 3.384300
##                                                                                                                                                                                                                                                stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT -8.420343
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG   7.325595
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  -7.126480
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT  7.292108
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  -6.724603
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT -6.961968
##                                                                                                                                                                                                                                                 pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.753834e-17
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  2.378407e-13
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  1.029686e-12
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.051422e-13
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  1.760713e-11
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 3.355510e-12
##                                                                                                                                                                                                                                                   padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1.163689e-14
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  1.843265e-11
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  3.546695e-11
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 1.891882e-11
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  2.274255e-10
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 7.240322e-11
##                                                                                                                                                                                                                                            Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  Bacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Bacteria
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
##                                                                                                                                                                                                                                                  Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG     Firmicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT     Firmicutes
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT    Firmicutes
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT     Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
##                                                                                                                                                                                                                                                   Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Negativicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  Negativicutes
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT    Clostridia
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Negativicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidia
##                                                                                                                                                                                                                                                     Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Selenomonadales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  Selenomonadales
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT   Clostridiales
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Selenomonadales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidales
##                                                                                                                                                                                                                                                       Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT     Prevotellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG     Veillonellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT     Veillonellaceae
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT    Ruminococcaceae
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Acidaminococcaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT     Bacteroidaceae
##                                                                                                                                                                                                                                                           Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT            Prevotella
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG              Dialister
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT              Megamonas
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT          Ruminococcus
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Phascolarctobacterium
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT           Bacteroides
##                                                                                                                                                                                                                                              Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT       <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG        <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  funiformis
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT       <NA>
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT     faecium
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT      dorei
write.table(sigtab_dds.dds.d.9.narrow, file="./results/deseq_d.9_narrow_rota_boost.txt", sep = "\t") # Change filename to save results to appropriate file

# Quick check of factor levels
mcols(res.dds.d.9.narrow, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                            description
##                                                            <character>
## baseMean                     mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE                  standard error: d7 rota boost updated Yes vs No
## stat                   Wald statistic: d7 rota boost updated Yes vs No
## pvalue              Wald test p-value: d7 rota boost updated Yes vs No
## padj                                              BH adjusted p-values
# Prepare to join results data.table and taxonomy table
resdt.dds.d.9.narrow = data.table(as(results(dds.d.9.narrow, cooksCutoff = FALSE), "data.frame"),
                   keep.rownames = TRUE)
setnames(resdt.dds.d.9.narrow, "rn", "OTU")
taxdt.dds.d.9.com = data.table(data.frame(as(tax_table(ps1.d.9.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d.9.com, "rn", "OTU")

# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d.9.com, "OTU")
setkeyv(resdt.dds.d.9.narrow, "OTU")
resdt.dds.d.9.narrow <- taxdt.dds.d.9.com[resdt.dds.d.9.narrow]
resdt.dds.d.9.narrow
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA  0.000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum  0.000000
##    3:    Fusobacteriaceae      Fusobacterium        NA  0.000000
##    4:       Rikenellaceae                 NA        NA  0.000000
##    5:      Eubacteriaceae        Eubacterium        NA  0.000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris 58.270669
## 1587:      Bacteroidaceae        Bacteroides        NA 52.257748
## 1588:      Prevotellaceae         Prevotella        NA  0.000000
## 1589:      Prevotellaceae         Prevotella     bivia  0.000000
## 1590: Methanobacteriaceae Methanobrevibacter        NA  4.821277
##       log2FoldChange    lfcSE      stat       pvalue         padj
##    1:             NA       NA        NA           NA           NA
##    2:             NA       NA        NA           NA           NA
##    3:             NA       NA        NA           NA           NA
##    4:             NA       NA        NA           NA           NA
##    5:             NA       NA        NA           NA           NA
##   ---                                                            
## 1586:      -23.82741 3.384139 -7.040908 1.909917e-12 4.933952e-11
## 1587:      -23.67565 3.384227 -6.995880 2.635985e-12 6.285811e-11
## 1588:             NA       NA        NA           NA           NA
## 1589:             NA       NA        NA           NA           NA
## 1590:        5.60415 3.182472  1.760942 7.824816e-02 2.241558e-01
resdt.dds.d.9.narrow[, Significant := padj < alpha]
resdt.dds.d.9.narrow[!is.na(Significant)]
##                                                                                                                                                                                                                                             OTU
##   1:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   2:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   3:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   4:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   5:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##  ---                                                                                                                                                                                                                                           
## 306:  TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCGGTTTCGTAAGTCGTGTGTGAAAGGCGGGGGCTCAACCCCCGGACTGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 307:  TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 308:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 309:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 310: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##       Kingdom          Phylum            Class              Order
##   1: Bacteria      Firmicutes       Clostridia      Clostridiales
##   2: Bacteria      Firmicutes       Clostridia      Clostridiales
##   3: Bacteria      Firmicutes       Clostridia      Clostridiales
##   4: Bacteria      Firmicutes       Clostridia      Clostridiales
##   5: Bacteria      Firmicutes       Clostridia      Clostridiales
##  ---                                                             
## 306: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 307: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 308: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 309: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 310:  Archaea   Euryarchaeota  Methanobacteria Methanobacteriales
##                   Family              Genus     Species    baseMean
##   1:     Ruminococcaceae   Faecalibacterium prausnitzii 2195.621485
##   2:     Ruminococcaceae   Faecalibacterium          NA   28.411359
##   3:     Ruminococcaceae   Faecalibacterium          NA   46.137588
##   4:     Ruminococcaceae   Faecalibacterium prausnitzii 1704.807731
##   5:     Ruminococcaceae   Faecalibacterium          NA    4.517713
##  ---                                                               
## 306: Verrucomicrobiaceae        Akkermansia          NA   23.562976
## 307: Verrucomicrobiaceae        Akkermansia muciniphila   27.933233
## 308:      Bacteroidaceae        Bacteroides   stercoris   58.270669
## 309:      Bacteroidaceae        Bacteroides          NA   52.257748
## 310: Methanobacteriaceae Methanobrevibacter          NA    4.821277
##      log2FoldChange    lfcSE       stat       pvalue         padj
##   1:      0.4403465 1.654648  0.2661270 7.901414e-01 9.493947e-01
##   2:    -22.7125700 3.384945 -6.7098791 1.947857e-11 2.322445e-10
##   3:     -9.0755154 3.384341 -2.6816199 7.326665e-03 2.949696e-02
##   4:      0.5329179 1.458388  0.3654157 7.148011e-01 9.436458e-01
##   5:      5.5171402 3.391411  1.6267981 1.037800e-01 2.485223e-01
##  ---                                                             
## 306:     21.7238114 3.384917  6.4178277 1.382326e-10 1.127687e-09
## 307:      1.6111951 3.234527  0.4981239 6.183967e-01 9.351365e-01
## 308:    -23.8274114 3.384139 -7.0409076 1.909917e-12 4.933952e-11
## 309:    -23.6756493 3.384227 -6.9958803 2.635985e-12 6.285811e-11
## 310:      5.6041500 3.182472  1.7609424 7.824816e-02 2.241558e-01
##      Significant
##   1:       FALSE
##   2:        TRUE
##   3:        TRUE
##   4:       FALSE
##   5:       FALSE
##  ---            
## 306:        TRUE
## 307:       FALSE
## 308:        TRUE
## 309:        TRUE
## 310:       FALSE
resdt.dds.d.9.narrow
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA  0.000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum  0.000000
##    3:    Fusobacteriaceae      Fusobacterium        NA  0.000000
##    4:       Rikenellaceae                 NA        NA  0.000000
##    5:      Eubacteriaceae        Eubacterium        NA  0.000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris 58.270669
## 1587:      Bacteroidaceae        Bacteroides        NA 52.257748
## 1588:      Prevotellaceae         Prevotella        NA  0.000000
## 1589:      Prevotellaceae         Prevotella     bivia  0.000000
## 1590: Methanobacteriaceae Methanobrevibacter        NA  4.821277
##       log2FoldChange    lfcSE      stat       pvalue         padj
##    1:             NA       NA        NA           NA           NA
##    2:             NA       NA        NA           NA           NA
##    3:             NA       NA        NA           NA           NA
##    4:             NA       NA        NA           NA           NA
##    5:             NA       NA        NA           NA           NA
##   ---                                                            
## 1586:      -23.82741 3.384139 -7.040908 1.909917e-12 4.933952e-11
## 1587:      -23.67565 3.384227 -6.995880 2.635985e-12 6.285811e-11
## 1588:             NA       NA        NA           NA           NA
## 1589:             NA       NA        NA           NA           NA
## 1590:        5.60415 3.182472  1.760942 7.824816e-02 2.241558e-01
##       Significant
##    1:          NA
##    2:          NA
##    3:          NA
##    4:          NA
##    5:          NA
##   ---            
## 1586:        TRUE
## 1587:        TRUE
## 1588:          NA
## 1589:          NA
## 1590:       FALSE
volcano.d.9.narrow.boost = ggplot(
  data = resdt.dds.d.9.narrow[!is.na(Significant)][(pvalue < 1)],
  mapping = aes(x = log2FoldChange,
                y = -log10(pvalue),
                color = Phylum,
                label = OTU, label1 = Genus)) +
  theme_bw() +
  geom_point() + 
  geom_point(data = resdt.dds.d.9.narrow[(Significant)], size = 7, alpha = 0.7) + 
  # geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
  theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
  geom_hline(yintercept = -log10(alpha)) +
  ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay -9 Narrow Spectrum Antibiotics ~ Rotavirus Boost") +
  theme(axis.title = element_text(size=12)) +
  theme(axis.text = element_text(size=12)) +
  theme(legend.text = element_text(size=12)) +
  geom_vline(xintercept = 0, lty = 2)
volcano.d.9.narrow.boost

summary(res.dds.d.9.narrow)
## 
## out of 469 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 46, 9.8% 
## LFC < 0 (down)   : 36, 7.7% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 159, 34% 
## (mean count < 4)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
mcols(res.dds.d.9.narrow, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                            description
##                                                            <character>
## baseMean                     mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE                  standard error: d7 rota boost updated Yes vs No
## stat                   Wald statistic: d7 rota boost updated Yes vs No
## pvalue              Wald test p-value: d7 rota boost updated Yes vs No
## padj                                              BH adjusted p-values
ggplotly(volcano.d.9.narrow.boost)

BOOST: Day 0 Narrow Spectrum Antibiotics

sample_data(ps1)$day
##   [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
##  [24] -9  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7
##  [47]  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  0  0  0
##  [70]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [93]  0  0  0  0  0  0  0  0
ps1.d0.narrow <- subset_samples(ps1.narrow, day == "0")
sample_data(ps1.d0.narrow)$day
##  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0
## Levels: 0
sample_data(ps1.d0.narrow)$randomization_arm
##  [1] Narrow spectrum antibiotics Narrow spectrum antibiotics
##  [3] Narrow spectrum antibiotics Narrow spectrum antibiotics
##  [5] Narrow spectrum antibiotics Narrow spectrum antibiotics
##  [7] Narrow spectrum antibiotics Narrow spectrum antibiotics
##  [9] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [11] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [13] Narrow spectrum antibiotics
## Levels: Narrow spectrum antibiotics
# Differential Abundance Testing
ds.d0.narrow <- phyloseq_to_deseq2(ps1.d0.narrow, ~d7_rota_boost_updated)

geoMeans.ds.d0.narrow <- apply(counts(ds.d0.narrow), 1, gm_mean)
ds.d0.narrow <- estimateSizeFactors(ds.d0.narrow, geoMeans = geoMeans.ds.d0.narrow)

dds.d0.narrow <- DESeq(ds.d0.narrow, test="Wald", fitType="local", betaPrior = FALSE)

alpha = 0.05

# Tabulate and write results
res.dds.d0.narrow = results(dds.d0.narrow, cooksCutoff = FALSE)
sigtab_dds.dds.d0.narrow = res.dds.d0.narrow[which(res.dds.d0.narrow$padj < alpha), ]
sigtab_dds.dds.d0.narrow = cbind(as(sigtab_dds.dds.d0.narrow, "data.frame"), as(tax_table(ps1.d0.narrow)[rownames(sigtab_dds.dds.d0.narrow), ], "matrix"))
summary(res.dds.d0.narrow)
## 
## out of 182 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 36, 20% 
## LFC < 0 (down)   : 4, 2.2% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 130, 71% 
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
head(sigtab_dds.dds.d0.narrow)
##                                                                                                                                                                                                                                              baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  703.511301
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG    4.606087
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT    6.889104
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   18.784824
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT   139.684130
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 1047.916550
##                                                                                                                                                                                                                                           log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT       9.034369
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG      20.603394
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT      21.161672
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT      22.552152
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT       25.349818
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC      26.872310
##                                                                                                                                                                                                                                              lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 2.912451
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 3.002982
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 3.000332
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 2.996913
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  2.995183
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 2.994950
##                                                                                                                                                                                                                                               stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.101982
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 6.860979
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 7.053109
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 7.525129
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  8.463528
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 8.972541
##                                                                                                                                                                                                                                                 pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1.922300e-03
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 6.839046e-12
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 1.749632e-12
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 5.266844e-14
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  2.594085e-17
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 2.897503e-19
##                                                                                                                                                                                                                                                   padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5.999905e-03
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 2.709314e-11
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 9.010606e-12
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 5.413726e-13
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  8.906360e-16
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 2.403841e-17
##                                                                                                                                                                                                                                            Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Bacteria
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Bacteria
##                                                                                                                                                                                                                                                  Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG    Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidetes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT     Firmicutes
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Synergistetes
##                                                                                                                                                                                                                                                   Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidia
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG    Clostridia
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT   Bacteroidia
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Negativicutes
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC   Synergistia
##                                                                                                                                                                                                                                                     Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidales
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG   Clostridiales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT   Bacteroidales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Selenomonadales
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC   Synergistales
##                                                                                                                                                                                                                                                       Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT     Prevotellaceae
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG    Lachnospiraceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT     Bacteroidaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT     Bacteroidaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Acidaminococcaceae
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC     Synergistaceae
##                                                                                                                                                                                                                                                     Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT      Prevotella
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG         Blautia
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT     Bacteroides
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT     Bacteroides
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Acidaminococcus
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC  Cloacibacillus
##                                                                                                                                                                                                                                             Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT     copri
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG      <NA>
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT    ovatus
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT     dorei
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT       <NA>
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC evryensis
write.table(sigtab_dds.dds.d0.narrow, file="./results/deseq_d7_narrow_rota_boost.txt", sep = "\t") # Change filename to save results to appropriate file

# Quick check of factor levels
mcols(res.dds.d0.narrow, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                            description
##                                                            <character>
## baseMean                     mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE                  standard error: d7 rota boost updated Yes vs No
## stat                   Wald statistic: d7 rota boost updated Yes vs No
## pvalue              Wald test p-value: d7 rota boost updated Yes vs No
## padj                                              BH adjusted p-values
# Prepare to join results data.table and taxonomy table
resdt.dds.d0.narrow = data.table(as(results(dds.d0.narrow, cooksCutoff = FALSE), "data.frame"),
                   keep.rownames = TRUE)
setnames(resdt.dds.d0.narrow, "rn", "OTU")
taxdt.dds.d0.com = data.table(data.frame(as(tax_table(ps1.d0.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d0.com, "rn", "OTU")

# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d0.com, "OTU")
setkeyv(resdt.dds.d0.narrow, "OTU")
resdt.dds.d0.narrow <- taxdt.dds.d0.com[resdt.dds.d0.narrow]
resdt.dds.d0.narrow
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA 0.0000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum 0.0000000
##    3:    Fusobacteriaceae      Fusobacterium        NA 0.3496783
##    4:       Rikenellaceae                 NA        NA 0.0000000
##    5:      Eubacteriaceae        Eubacterium        NA 0.0000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris 0.0000000
## 1587:      Bacteroidaceae        Bacteroides        NA 0.0000000
## 1588:      Prevotellaceae         Prevotella        NA 0.0000000
## 1589:      Prevotellaceae         Prevotella     bivia 2.6389631
## 1590: Methanobacteriaceae Methanobrevibacter        NA 7.1099698
##       log2FoldChange    lfcSE       stat     pvalue       padj
##    1:             NA       NA         NA         NA         NA
##    2:             NA       NA         NA         NA         NA
##    3:      -1.711694 3.066810 -0.5581352 0.57675209         NA
##    4:             NA       NA         NA         NA         NA
##    5:             NA       NA         NA         NA         NA
##   ---                                                         
## 1586:             NA       NA         NA         NA         NA
## 1587:             NA       NA         NA         NA         NA
## 1588:             NA       NA         NA         NA         NA
## 1589:      -4.497915 3.013771 -1.4924542 0.13558011 0.23669071
## 1590:       6.507048 3.000192  2.1688775 0.03009199 0.08156512
resdt.dds.d0.narrow[, Significant := padj < alpha]
resdt.dds.d0.narrow[!is.na(Significant)]
##                                                                                                                                                                                                                                             OTU
##   1:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   2:  CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGCCCCTTAAGCGTGTTGTGAAATGCCGCGGCTCAACCGTGGCACTGCAGCGCGAACTGGGGGGCTTGAGTGCACGCAACGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTGCGGGAGTGCGACTGACGCTGAAGCTCGAAGGTGCGGGT
##   3:  CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGCCCCTTAAGCGTGTTGTGAAATGCCGCGGCTCAACCGTGGCACTGCAGCGCGAACTGGGGGGCTTGAGTGCACGCAACGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGTAGCTTGCGGGAGTGCGACTGACGCTGAAGCTCGAAGGTGCGGGT
##   4:  CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGCCCCTTAAGCGTGTTGTGAAATGCCGCGGCTCAACCGTGGCACTGCAGCGCGAACTGGGGGGCTTGAGTGCACGCAACGCAGGTGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTGCGGGAGTGCGACTGACGCTGAAGCTCGAAGGTGCGGGT
##   5:  CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCTGGAGATTAAGTGTGTTGTGAAATGTAGACGCTCAACGTCTGAATTGCAGCGCATACTGGTTTCCTTGAGTACGCACAACGTTGGCGGAATTCGTCGTGTAGCGGTGAAATGCTTAGATATGACGAAGAACTCCGATTGCGAAGGCAGCTGACGGGAGCGCAACTGACGCTTAAGCTCGAAGGTGCGGGT
##  ---                                                                                                                                                                                                                                           
##  99:  TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATCCCGGGGCTTAACTCCGGAACTGCCTCTAATACTGTTAGACTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 100:  TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCGGTTTCGTAAGTCGTGTGTGAAAGGCGGGGGCTCAACCCCCGGACTGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 101:  TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 102:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 103: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##       Kingdom          Phylum            Class              Order
##   1: Bacteria      Firmicutes       Clostridia      Clostridiales
##   2: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
##   3: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
##   4: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
##   5: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
##  ---                                                             
##  99: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 100: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 101: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 102: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 103:  Archaea   Euryarchaeota  Methanobacteria Methanobacteriales
##                   Family              Genus        Species    baseMean
##   1:     Ruminococcaceae   Faecalibacterium    prausnitzii    3.134710
##   2:      Prevotellaceae         Prevotella             NA   15.059902
##   3:      Prevotellaceae         Prevotella             NA    7.069342
##   4:      Prevotellaceae         Prevotella             NA   15.320246
##   5:      Prevotellaceae         Prevotella melaninogenica    4.500581
##  ---                                                                  
##  99:       Rikenellaceae          Alistipes             NA    2.182885
## 100: Verrucomicrobiaceae        Akkermansia             NA  370.893878
## 101: Verrucomicrobiaceae        Akkermansia    muciniphila 1514.314987
## 102:      Prevotellaceae         Prevotella          bivia    2.638963
## 103: Methanobacteriaceae Methanobrevibacter             NA    7.109970
##      log2FoldChange    lfcSE       stat       pvalue         padj
##   1:      5.3287520 3.006810  1.7722278 7.635674e-02 1.747721e-01
##   2:     20.7492055 2.997405  6.9223889 4.440902e-12 1.905887e-11
##   3:     19.6246997 3.000196  6.5411383 6.105234e-11 2.028513e-10
##   4:     22.2698847 2.997363  7.4298266 1.087401e-13 8.000167e-13
##   5:     -1.5595525 2.940371 -0.5303932 5.958394e-01 6.941314e-01
##  ---                                                             
##  99:      4.8284659 3.011690  1.6032412 1.088814e-01 2.156690e-01
## 100:     26.7151976 2.995015  8.9198867 4.667653e-19 2.403841e-17
## 101:     -0.5705423 2.894036 -0.1971442 8.437147e-01 8.959033e-01
## 102:     -4.4979152 3.013771 -1.4924542 1.355801e-01 2.366907e-01
## 103:      6.5070483 3.000192  2.1688775 3.009199e-02 8.156512e-02
##      Significant
##   1:       FALSE
##   2:        TRUE
##   3:        TRUE
##   4:        TRUE
##   5:       FALSE
##  ---            
##  99:       FALSE
## 100:        TRUE
## 101:       FALSE
## 102:       FALSE
## 103:       FALSE
resdt.dds.d0.narrow
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA 0.0000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum 0.0000000
##    3:    Fusobacteriaceae      Fusobacterium        NA 0.3496783
##    4:       Rikenellaceae                 NA        NA 0.0000000
##    5:      Eubacteriaceae        Eubacterium        NA 0.0000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris 0.0000000
## 1587:      Bacteroidaceae        Bacteroides        NA 0.0000000
## 1588:      Prevotellaceae         Prevotella        NA 0.0000000
## 1589:      Prevotellaceae         Prevotella     bivia 2.6389631
## 1590: Methanobacteriaceae Methanobrevibacter        NA 7.1099698
##       log2FoldChange    lfcSE       stat     pvalue       padj Significant
##    1:             NA       NA         NA         NA         NA          NA
##    2:             NA       NA         NA         NA         NA          NA
##    3:      -1.711694 3.066810 -0.5581352 0.57675209         NA          NA
##    4:             NA       NA         NA         NA         NA          NA
##    5:             NA       NA         NA         NA         NA          NA
##   ---                                                                     
## 1586:             NA       NA         NA         NA         NA          NA
## 1587:             NA       NA         NA         NA         NA          NA
## 1588:             NA       NA         NA         NA         NA          NA
## 1589:      -4.497915 3.013771 -1.4924542 0.13558011 0.23669071       FALSE
## 1590:       6.507048 3.000192  2.1688775 0.03009199 0.08156512       FALSE
volcano.d0.narrow.boost = ggplot(
  data = resdt.dds.d0.narrow[!is.na(Significant)][(pvalue < 1)],
  mapping = aes(x = log2FoldChange,
                y = -log10(pvalue),
                color = Phylum,
                label = OTU, label1 = Genus)) +
  theme_bw() +
  geom_point() + 
  geom_point(data = resdt.dds.d0.narrow[(Significant)], size = 7, alpha = 0.7) + 
  # geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
  theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
  geom_hline(yintercept = -log10(alpha)) +
  ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 0 Narrow Spectrum Antibiotics ~ Rotavirus Boost") +
  theme(axis.title = element_text(size=12)) +
  theme(axis.text = element_text(size=12)) +
  theme(legend.text = element_text(size=12)) +
  geom_vline(xintercept = 0, lty = 2)
volcano.d0.narrow.boost

summary(res.dds.d0.narrow)
## 
## out of 182 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 36, 20% 
## LFC < 0 (down)   : 4, 2.2% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 130, 71% 
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
mcols(res.dds.d0.narrow, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                            description
##                                                            <character>
## baseMean                     mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE                  standard error: d7 rota boost updated Yes vs No
## stat                   Wald statistic: d7 rota boost updated Yes vs No
## pvalue              Wald test p-value: d7 rota boost updated Yes vs No
## padj                                              BH adjusted p-values
ggplotly(volcano.d0.narrow.boost)

BOOST: Day 7 Narrow Spectrum Antibiotics

sample_data(ps1)$day
##   [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
##  [24] -9  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7
##  [47]  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  0  0  0
##  [70]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [93]  0  0  0  0  0  0  0  0
ps1.d7.narrow <- subset_samples(ps1.narrow, day == "7")
sample_data(ps1.d7.narrow)$day
##  [1] 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
## Levels: 7
sample_data(ps1.d7.narrow)$randomization_arm
##  [1] Narrow spectrum antibiotics Narrow spectrum antibiotics
##  [3] Narrow spectrum antibiotics Narrow spectrum antibiotics
##  [5] Narrow spectrum antibiotics Narrow spectrum antibiotics
##  [7] Narrow spectrum antibiotics Narrow spectrum antibiotics
##  [9] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [11] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [13] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [15] Narrow spectrum antibiotics
## Levels: Narrow spectrum antibiotics
# Differential Abundance Testing
ds.d7.narrow <- phyloseq_to_deseq2(ps1.d7.narrow, ~d7_rota_boost_updated)

geoMeans.ds.d7.narrow <- apply(counts(ds.d7.narrow), 1, gm_mean)
ds.d7.narrow <- estimateSizeFactors(ds.d7.narrow, geoMeans = geoMeans.ds.d7.narrow)

dds.d7.narrow <- DESeq(ds.d7.narrow, test="Wald", fitType="local", betaPrior = FALSE)

alpha = 0.05

# Tabulate and write results
res.dds.d7.narrow = results(dds.d7.narrow, cooksCutoff = FALSE)
sigtab_dds.dds.d7.narrow = res.dds.d7.narrow[which(res.dds.d7.narrow$padj < alpha), ]
sigtab_dds.dds.d7.narrow = cbind(as(sigtab_dds.dds.d7.narrow, "data.frame"), as(tax_table(ps1.d7.narrow)[rownames(sigtab_dds.dds.d7.narrow), ], "matrix"))
summary(res.dds.d7.narrow)
## 
## out of 538 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 160, 30% 
## LFC < 0 (down)   : 16, 3% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 379, 70% 
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
head(sigtab_dds.dds.d7.narrow)
##                                                                                                                                                                                                                                             baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 2897.92173
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  1047.66115
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT   172.92756
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT  343.72024
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   42.07216
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT   71.32087
##                                                                                                                                                                                                                                           log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT      11.278714
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG       28.626919
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT      -25.437960
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT      26.344992
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT      24.028972
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT       7.212213
##                                                                                                                                                                                                                                              lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 2.958993
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  3.022391
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  3.060524
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.022442
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 3.022981
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 2.648139
##                                                                                                                                                                                                                                                stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  3.811673
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG   9.471613
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  -8.311635
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT  8.716460
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT  7.948766
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT  2.723503
##                                                                                                                                                                                                                                                 pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1.380297e-04
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  2.755559e-21
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  9.439256e-17
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 2.870359e-18
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 1.883782e-15
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 6.459372e-03
##                                                                                                                                                                                                                                                   padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 4.090237e-04
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  8.900455e-19
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  2.771709e-15
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.090420e-16
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 2.535256e-14
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 1.783228e-02
##                                                                                                                                                                                                                                            Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Bacteria
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  Bacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Bacteria
##                                                                                                                                                                                                                                                  Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG     Firmicutes
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT   Fusobacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT    Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT    Firmicutes
##                                                                                                                                                                                                                                                   Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Negativicutes
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  Fusobacteriia
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT    Clostridia
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidia
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT    Clostridia
##                                                                                                                                                                                                                                                     Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Selenomonadales
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  Fusobacteriales
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT   Clostridiales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidales
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT   Clostridiales
##                                                                                                                                                                                                                                                     Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Prevotellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG   Veillonellaceae
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  Fusobacteriaceae
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT  Ruminococcaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidaceae
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT  Ruminococcaceae
##                                                                                                                                                                                                                                                      Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT       Prevotella
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG         Dialister
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT     Fusobacterium
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT     Ruminococcus
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT      Bacteroides
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Faecalibacterium
##                                                                                                                                                                                                                                               Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT        <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG         <NA>
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT         <NA>
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT        <NA>
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT       dorei
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT prausnitzii
write.table(sigtab_dds.dds.d7.narrow, file="./results/deseq_d7_narrow_rota_boost.txt", sep = "\t") # Change filename to save results to appropriate file

# Quick check of factor levels
mcols(res.dds.d7.narrow, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                            description
##                                                            <character>
## baseMean                     mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE                  standard error: d7 rota boost updated Yes vs No
## stat                   Wald statistic: d7 rota boost updated Yes vs No
## pvalue              Wald test p-value: d7 rota boost updated Yes vs No
## padj                                              BH adjusted p-values
# Prepare to join results data.table and taxonomy table
resdt.dds.d7.narrow = data.table(as(results(dds.d7.narrow, cooksCutoff = FALSE), "data.frame"),
                   keep.rownames = TRUE)
setnames(resdt.dds.d7.narrow, "rn", "OTU")
taxdt.dds.d7.com = data.table(data.frame(as(tax_table(ps1.d7.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d7.com, "rn", "OTU")

# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d7.com, "OTU")
setkeyv(resdt.dds.d7.narrow, "OTU")
resdt.dds.d7.narrow <- taxdt.dds.d7.com[resdt.dds.d7.narrow]
resdt.dds.d7.narrow
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA  0.000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum  0.000000
##    3:    Fusobacteriaceae      Fusobacterium        NA  0.000000
##    4:       Rikenellaceae                 NA        NA  0.000000
##    5:      Eubacteriaceae        Eubacterium        NA  0.000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris  0.000000
## 1587:      Bacteroidaceae        Bacteroides        NA  0.000000
## 1588:      Prevotellaceae         Prevotella        NA 28.552648
## 1589:      Prevotellaceae         Prevotella     bivia  0.000000
## 1590: Methanobacteriaceae Methanobrevibacter        NA  3.401384
##       log2FoldChange    lfcSE     stat       pvalue         padj
##    1:             NA       NA       NA           NA           NA
##    2:       0.000000 0.000000 0.000000 1.000000e+00           NA
##    3:             NA       NA       NA           NA           NA
##    4:             NA       NA       NA           NA           NA
##    5:             NA       NA       NA           NA           NA
##   ---                                                           
## 1586:             NA       NA       NA           NA           NA
## 1587:             NA       NA       NA           NA           NA
## 1588:      23.590829 3.023272 7.803079 6.041479e-15 6.366766e-14
## 1589:             NA       NA       NA           NA           NA
## 1590:       3.813212 3.015695 1.264455 2.060666e-01 2.856632e-01
resdt.dds.d7.narrow[, Significant := padj < alpha]
resdt.dds.d7.narrow[!is.na(Significant)]
##                                                                                                                                                                                                                                             OTU
##   1:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   2:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   3:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGATAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   4:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   5:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTATGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##  ---                                                                                                                                                                                                                                           
## 319:  TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATCCCGGGGCTTAACTCCGGAACTGCCTCTAATACTGTTAGACTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 320:  TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCAACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 321:  TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 322:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 323: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##       Kingdom          Phylum            Class              Order
##   1: Bacteria      Firmicutes       Clostridia      Clostridiales
##   2: Bacteria      Firmicutes       Clostridia      Clostridiales
##   3: Bacteria      Firmicutes       Clostridia      Clostridiales
##   4: Bacteria      Firmicutes       Clostridia      Clostridiales
##   5: Bacteria      Firmicutes       Clostridia      Clostridiales
##  ---                                                             
## 319: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 320: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 321: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 322: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 323:  Archaea   Euryarchaeota  Methanobacteria Methanobacteriales
##                   Family              Genus     Species    baseMean
##   1:     Ruminococcaceae   Faecalibacterium prausnitzii  732.822816
##   2:     Ruminococcaceae   Faecalibacterium prausnitzii 1160.314775
##   3:     Ruminococcaceae   Faecalibacterium          NA    8.445825
##   4:     Ruminococcaceae   Faecalibacterium prausnitzii  134.830487
##   5:     Ruminococcaceae   Faecalibacterium          NA    2.687308
##  ---                                                               
## 319:       Rikenellaceae          Alistipes          NA    8.007783
## 320:       Rikenellaceae          Alistipes  putredinis   47.151212
## 321: Verrucomicrobiaceae        Akkermansia muciniphila 3634.940803
## 322:      Prevotellaceae         Prevotella          NA   28.552648
## 323: Methanobacteriaceae Methanobrevibacter          NA    3.401384
##      log2FoldChange    lfcSE       stat       pvalue         padj
##   1:      5.7268242 2.946129  1.9438472 5.191388e-02 9.891567e-02
##   2:     -0.6759581 2.689203 -0.2513601 8.015357e-01 8.598082e-01
##   3:     21.8940007 3.025423  7.2366751 4.598178e-13 1.856514e-12
##   4:      4.5457648 2.681134  1.6954632 8.998758e-02 1.345648e-01
##   5:      5.2675987 3.031928  1.7373759 8.232085e-02 1.254228e-01
##  ---                                                             
## 319:      0.5810587 2.957649  0.1964596 8.442504e-01 8.882504e-01
## 320:      7.0543802 2.989416  2.3597853 1.828551e-02 4.724977e-02
## 321:     -0.9299005 2.733387 -0.3402008 7.337053e-01 8.060776e-01
## 322:     23.5908286 3.023272  7.8030788 6.041479e-15 6.366766e-14
## 323:      3.8132121 3.015695  1.2644553 2.060666e-01 2.856632e-01
##      Significant
##   1:       FALSE
##   2:       FALSE
##   3:        TRUE
##   4:       FALSE
##   5:       FALSE
##  ---            
## 319:       FALSE
## 320:        TRUE
## 321:       FALSE
## 322:        TRUE
## 323:       FALSE
resdt.dds.d7.narrow
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA  0.000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum  0.000000
##    3:    Fusobacteriaceae      Fusobacterium        NA  0.000000
##    4:       Rikenellaceae                 NA        NA  0.000000
##    5:      Eubacteriaceae        Eubacterium        NA  0.000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris  0.000000
## 1587:      Bacteroidaceae        Bacteroides        NA  0.000000
## 1588:      Prevotellaceae         Prevotella        NA 28.552648
## 1589:      Prevotellaceae         Prevotella     bivia  0.000000
## 1590: Methanobacteriaceae Methanobrevibacter        NA  3.401384
##       log2FoldChange    lfcSE     stat       pvalue         padj
##    1:             NA       NA       NA           NA           NA
##    2:       0.000000 0.000000 0.000000 1.000000e+00           NA
##    3:             NA       NA       NA           NA           NA
##    4:             NA       NA       NA           NA           NA
##    5:             NA       NA       NA           NA           NA
##   ---                                                           
## 1586:             NA       NA       NA           NA           NA
## 1587:             NA       NA       NA           NA           NA
## 1588:      23.590829 3.023272 7.803079 6.041479e-15 6.366766e-14
## 1589:             NA       NA       NA           NA           NA
## 1590:       3.813212 3.015695 1.264455 2.060666e-01 2.856632e-01
##       Significant
##    1:          NA
##    2:          NA
##    3:          NA
##    4:          NA
##    5:          NA
##   ---            
## 1586:          NA
## 1587:          NA
## 1588:        TRUE
## 1589:          NA
## 1590:       FALSE
volcano.d7.narrow.boost = ggplot(
  data = resdt.dds.d7.narrow[!is.na(Significant)][(pvalue < 1)],
  mapping = aes(x = log2FoldChange,
                y = -log10(pvalue),
                color = Phylum,
                label = OTU, label1 = Genus)) +
  theme_bw() +
  geom_point() + 
  geom_point(data = resdt.dds.d7.narrow[(Significant)], size = 7, alpha = 0.7) + 
  # geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
  theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
  geom_hline(yintercept = -log10(alpha)) +
  ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 7 Narrow Spectrum Antibiotics ~ Rotavirus Boost") +
  theme(axis.title = element_text(size=12)) +
  theme(axis.text = element_text(size=12)) +
  theme(legend.text = element_text(size=12)) +
  geom_vline(xintercept = 0, lty = 2)
volcano.d7.narrow.boost

summary(res.dds.d7.narrow)
## 
## out of 538 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 160, 30% 
## LFC < 0 (down)   : 16, 3% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 379, 70% 
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
mcols(res.dds.d7.narrow, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                            description
##                                                            <character>
## baseMean                     mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE                  standard error: d7 rota boost updated Yes vs No
## stat                   Wald statistic: d7 rota boost updated Yes vs No
## pvalue              Wald test p-value: d7 rota boost updated Yes vs No
## padj                                              BH adjusted p-values
ggplotly(volcano.d7.narrow.boost)
grid.arrange(volcano.d.9.narrow.boost, volcano.d0.narrow.boost, volcano.d7.narrow.boost, ncol = 3)

Shedding

Shedding: Day -9 Narrow Spectrum Antibiotics

# Differential Abundance Testing
ds.d.9.narrow.shed <- phyloseq_to_deseq2(ps1.d.9.narrow, ~Shedding)

geoMeans.ds.d.9.narrow.shed <- apply(counts(ds.d.9.narrow.shed), 1, gm_mean)
ds.d.9.narrow.shed <- estimateSizeFactors(ds.d.9.narrow.shed, geoMeans = geoMeans.ds.d.9.narrow.shed)

dds.d.9.narrow.shed <- DESeq(ds.d.9.narrow.shed, test="Wald", fitType="local", betaPrior = FALSE)

alpha = 0.05

# Tabulate and write results
res.dds.d.9.narrow.shed = results(dds.d.9.narrow.shed, cooksCutoff = FALSE)
sigtab_dds.dds.d.9.narrow.shed = res.dds.d.9.narrow.shed[which(res.dds.d.9.narrow.shed$padj < alpha), ]
sigtab_dds.dds.d.9.narrow.shed = cbind(as(sigtab_dds.dds.d.9.narrow.shed, "data.frame"), as(tax_table(ps1.d.9.narrow)[rownames(sigtab_dds.dds.d.9.narrow.shed), ], "matrix"))
summary(res.dds.d.9.narrow.shed)
## 
## out of 469 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 24, 5.1% 
## LFC < 0 (down)   : 70, 15% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 135, 29% 
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
head(sigtab_dds.dds.d.9.narrow.shed)
##                                                                                                                                                                                                                                             baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1766.32988
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG   212.08362
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT    72.68788
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT   71.09135
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT  181.72015
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT    26.67661
##                                                                                                                                                                                                                                           log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT       28.71103
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG       -24.39424
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT        10.29535
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT      -22.90626
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT      -24.19062
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT        22.85897
##                                                                                                                                                                                                                                              lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.454425
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  3.533967
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  3.455110
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 3.534263
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 3.533992
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  3.456344
##                                                                                                                                                                                                                                                stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  8.311378
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  -6.902792
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT   2.979746
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT -6.481198
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT -6.845127
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT   6.613627
##                                                                                                                                                                                                                                                 pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 9.459736e-17
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  5.099043e-12
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  2.884876e-03
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 9.099746e-11
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 7.640795e-12
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  3.750147e-11
##                                                                                                                                                                                                                                                   padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.159552e-14
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  2.838467e-10
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  1.160902e-02
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 1.321441e-09
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 3.190032e-10
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  7.828433e-10
##                                                                                                                                                                                                                                            Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteria
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Bacteria
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Bacteria
##                                                                                                                                                                                                                                                  Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG     Firmicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT     Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidetes
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT    Firmicutes
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT     Firmicutes
##                                                                                                                                                                                                                                                   Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Negativicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  Negativicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT   Bacteroidia
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT    Clostridia
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Negativicutes
##                                                                                                                                                                                                                                                     Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Selenomonadales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT  Selenomonadales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT   Bacteroidales
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT   Clostridiales
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Selenomonadales
##                                                                                                                                                                                                                                                       Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT     Prevotellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG     Veillonellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT     Veillonellaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT     Bacteroidaceae
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT    Ruminococcaceae
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Acidaminococcaceae
##                                                                                                                                                                                                                                                           Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT            Prevotella
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG              Dialister
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT              Megamonas
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT           Bacteroides
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT      Faecalibacterium
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Phascolarctobacterium
##                                                                                                                                                                                                                                               Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT        <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG         <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT   funiformis
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT      ovatus
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT prausnitzii
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT      faecium
write.table(sigtab_dds.dds.d.9.narrow.shed, file="./results/deseq_d.9_narrow_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file

# Quick check of factor levels
mcols(res.dds.d.9.narrow.shed, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
# Prepare to join results data.table and taxonomy table
resdt.dds.d.9.narrow.shed = data.table(as(results(dds.d.9.narrow.shed, cooksCutoff = FALSE), "data.frame"),
                   keep.rownames = TRUE)
setnames(resdt.dds.d.9.narrow.shed, "rn", "OTU")
taxdt.dds.d.9.com = data.table(data.frame(as(tax_table(ps1.d.9.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d.9.com, "rn", "OTU")

# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d.9.com, "OTU")
setkeyv(resdt.dds.d.9.narrow.shed, "OTU")
resdt.dds.d.9.narrow.shed <- taxdt.dds.d.9.com[resdt.dds.d.9.narrow.shed]
resdt.dds.d.9.narrow.shed
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA  0.000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum  0.000000
##    3:    Fusobacteriaceae      Fusobacterium        NA  0.000000
##    4:       Rikenellaceae                 NA        NA  0.000000
##    5:      Eubacteriaceae        Eubacterium        NA  0.000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris 58.270669
## 1587:      Bacteroidaceae        Bacteroides        NA 52.257748
## 1588:      Prevotellaceae         Prevotella        NA  0.000000
## 1589:      Prevotellaceae         Prevotella     bivia  0.000000
## 1590: Methanobacteriaceae Methanobrevibacter        NA  4.821277
##       log2FoldChange    lfcSE       stat       pvalue         padj
##    1:             NA       NA         NA           NA           NA
##    2:             NA       NA         NA           NA           NA
##    3:             NA       NA         NA           NA           NA
##    4:             NA       NA         NA           NA           NA
##    5:             NA       NA         NA           NA           NA
##   ---                                                             
## 1586:      -22.64520 3.534361 -6.4071542 1.482609e-10 1.980765e-09
## 1587:      -22.49760 3.534424 -6.3652800 1.949338e-10 2.325282e-09
## 1588:             NA       NA         NA           NA           NA
## 1589:             NA       NA         NA           NA           NA
## 1590:       -2.77656 3.465376 -0.8012292 4.229990e-01 6.825201e-01
resdt.dds.d.9.narrow.shed[, Significant := padj < alpha]
resdt.dds.d.9.narrow.shed[!is.na(Significant)]
##                                                                                                                                                                                                                                             OTU
##   1:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   2:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   3:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   4:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   5:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##  ---                                                                                                                                                                                                                                           
## 330:  TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCGGTTTCGTAAGTCGTGTGTGAAAGGCGGGGGCTCAACCCCCGGACTGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 331:  TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 332:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 333:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 334: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##       Kingdom          Phylum            Class              Order
##   1: Bacteria      Firmicutes       Clostridia      Clostridiales
##   2: Bacteria      Firmicutes       Clostridia      Clostridiales
##   3: Bacteria      Firmicutes       Clostridia      Clostridiales
##   4: Bacteria      Firmicutes       Clostridia      Clostridiales
##   5: Bacteria      Firmicutes       Clostridia      Clostridiales
##  ---                                                             
## 330: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 331: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 332: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 333: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 334:  Archaea   Euryarchaeota  Methanobacteria Methanobacteriales
##                   Family              Genus     Species    baseMean
##   1:     Ruminococcaceae   Faecalibacterium prausnitzii 2195.621485
##   2:     Ruminococcaceae   Faecalibacterium          NA   28.411359
##   3:     Ruminococcaceae   Faecalibacterium          NA   46.137588
##   4:     Ruminococcaceae   Faecalibacterium prausnitzii 1704.807731
##   5:     Ruminococcaceae   Faecalibacterium          NA    4.517713
##  ---                                                               
## 330: Verrucomicrobiaceae        Akkermansia          NA   23.562976
## 331: Verrucomicrobiaceae        Akkermansia muciniphila   27.933233
## 332:      Bacteroidaceae        Bacteroides   stercoris   58.270669
## 333:      Bacteroidaceae        Bacteroides          NA   52.257748
## 334: Methanobacteriaceae Methanobrevibacter          NA    4.821277
##      log2FoldChange    lfcSE       stat       pvalue         padj
##   1:      0.5439154 1.705522  0.3189143 7.497915e-01 9.089230e-01
##   2:     22.9451456 3.456224  6.6387907 3.162671e-11 7.042214e-10
##   3:     -0.5440902 3.336748 -0.1630600 8.704712e-01 9.635057e-01
##   4:      0.3760386 1.508691  0.2492482 8.031688e-01 9.200151e-01
##   5:     -4.8752594 3.540803 -1.3768794 1.685495e-01 3.525053e-01
##  ---                                                             
## 330:    -21.4181238 3.535161 -6.0585990 1.373122e-09 9.970060e-09
## 331:      0.3623402 3.338275  0.1085411 9.135664e-01 9.758427e-01
## 332:    -22.6451975 3.534361 -6.4071542 1.482609e-10 1.980765e-09
## 333:    -22.4975970 3.534424 -6.3652800 1.949338e-10 2.325282e-09
## 334:     -2.7765605 3.465376 -0.8012292 4.229990e-01 6.825201e-01
##      Significant
##   1:       FALSE
##   2:        TRUE
##   3:       FALSE
##   4:       FALSE
##   5:       FALSE
##  ---            
## 330:        TRUE
## 331:       FALSE
## 332:        TRUE
## 333:        TRUE
## 334:       FALSE
resdt.dds.d.9.narrow.shed
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA  0.000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum  0.000000
##    3:    Fusobacteriaceae      Fusobacterium        NA  0.000000
##    4:       Rikenellaceae                 NA        NA  0.000000
##    5:      Eubacteriaceae        Eubacterium        NA  0.000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris 58.270669
## 1587:      Bacteroidaceae        Bacteroides        NA 52.257748
## 1588:      Prevotellaceae         Prevotella        NA  0.000000
## 1589:      Prevotellaceae         Prevotella     bivia  0.000000
## 1590: Methanobacteriaceae Methanobrevibacter        NA  4.821277
##       log2FoldChange    lfcSE       stat       pvalue         padj
##    1:             NA       NA         NA           NA           NA
##    2:             NA       NA         NA           NA           NA
##    3:             NA       NA         NA           NA           NA
##    4:             NA       NA         NA           NA           NA
##    5:             NA       NA         NA           NA           NA
##   ---                                                             
## 1586:      -22.64520 3.534361 -6.4071542 1.482609e-10 1.980765e-09
## 1587:      -22.49760 3.534424 -6.3652800 1.949338e-10 2.325282e-09
## 1588:             NA       NA         NA           NA           NA
## 1589:             NA       NA         NA           NA           NA
## 1590:       -2.77656 3.465376 -0.8012292 4.229990e-01 6.825201e-01
##       Significant
##    1:          NA
##    2:          NA
##    3:          NA
##    4:          NA
##    5:          NA
##   ---            
## 1586:        TRUE
## 1587:        TRUE
## 1588:          NA
## 1589:          NA
## 1590:       FALSE
volcano.d.9.narrow.shed = ggplot(
  data = resdt.dds.d.9.narrow.shed[!is.na(Significant)][(pvalue < 1)],
  mapping = aes(x = log2FoldChange,
                y = -log10(pvalue),
                color = Phylum,
                label = OTU, label1 = Genus)) +
  theme_bw() +
  geom_point() + 
  geom_point(data = resdt.dds.d.9.narrow.shed[(Significant)], size = 7, alpha = 0.7) + 
  # geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
  theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
  geom_hline(yintercept = -log10(alpha)) +
  ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay -9 Narrow Spectrum Antibiotics ~ Shedding") +
  theme(axis.title = element_text(size=12)) +
  theme(axis.text = element_text(size=12)) +
  theme(legend.text = element_text(size=12)) +
  geom_vline(xintercept = 0, lty = 2)
volcano.d.9.narrow.shed

summary(res.dds.d.9.narrow.shed)
## 
## out of 469 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 24, 5.1% 
## LFC < 0 (down)   : 70, 15% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 135, 29% 
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
mcols(res.dds.d.9.narrow.shed, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
ggplotly(volcano.d.9.narrow.shed)

Shedding: Day -9 Broad Spectrum Antibiotics

sample_data(ps1)$day
##   [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
##  [24] -9  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7
##  [47]  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  0  0  0
##  [70]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [93]  0  0  0  0  0  0  0  0
ps1.d.9.broad <- subset_samples(ps1.broad, day == "-9")
sample_data(ps1.d.9.broad)$day
## [1] -9 -9 -9 -9 -9 -9 -9
## Levels: -9
sample_data(ps1.d.9.broad)$randomization_arm
## [1] Broad spectrum antibiotics Broad spectrum antibiotics
## [3] Broad spectrum antibiotics Broad spectrum antibiotics
## [5] Broad spectrum antibiotics Broad spectrum antibiotics
## [7] Broad spectrum antibiotics
## Levels: Broad spectrum antibiotics
# Differential Abundance Testing
ds.d.9.broad <- phyloseq_to_deseq2(ps1.d.9.broad, ~Shedding)

geoMeans.ds.d.9.broad <- apply(counts(ds.d.9.broad), 1, gm_mean)
ds.d.9.broad <- estimateSizeFactors(ds.d.9.broad, geoMeans = geoMeans.ds.d.9.broad)

dds.d.9.broad <- DESeq(ds.d.9.broad, test="Wald", fitType="local", betaPrior = FALSE)

alpha = 0.05

# Tabulate and write results
res.dds.d.9.broad = results(dds.d.9.broad, cooksCutoff = FALSE)
sigtab_dds.dds.d.9.broad = res.dds.d.9.broad[which(res.dds.d.9.broad$padj < alpha), ]
sigtab_dds.dds.d.9.broad = cbind(as(sigtab_dds.dds.d.9.broad, "data.frame"), as(tax_table(ps1.d.9.broad)[rownames(sigtab_dds.dds.d.9.broad), ], "matrix"))
summary(res.dds.d.9.broad)
## 
## out of 464 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 1, 0.22% 
## LFC < 0 (down)   : 76, 16% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 0, 0% 
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
head(sigtab_dds.dds.d.9.broad)
##                                                                                                                                                                                                                                            baseMean
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT  358.3718
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1143.4846
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG   263.9524
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT  613.9829
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT  136.5218
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG  124.0001
##                                                                                                                                                                                                                                           log2FoldChange
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT     -11.077215
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT     -25.168109
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG      -21.221568
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT     -24.209249
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT      -9.684908
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG     -21.848371
##                                                                                                                                                                                                                                              lfcSE
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 3.475980
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5.333306
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  5.333438
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 5.333340
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.477524
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG 5.333631
##                                                                                                                                                                                                                                                stat
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT -3.186789
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT -4.719044
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  -3.978966
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT -4.539228
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT -2.785001
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG -4.096341
##                                                                                                                                                                                                                                                 pvalue
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 1.438616e-03
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 2.369551e-06
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  6.921561e-05
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 5.646051e-06
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 5.352757e-03
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG 4.197310e-05
##                                                                                                                                                                                                                                                  padj
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 0.009816442
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 0.001099472
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  0.002316514
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.001309884
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 0.034981398
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG 0.001989000
##                                                                                                                                                                                                                                            Kingdom
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Bacteria
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Bacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Bacteria
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG Bacteria
##                                                                                                                                                                                                                                                  Phylum
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG     Firmicutes
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT    Firmicutes
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT    Firmicutes
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG    Firmicutes
##                                                                                                                                                                                                                                                   Class
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidia
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Negativicutes
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT    Clostridia
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT    Clostridia
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG    Clostridia
##                                                                                                                                                                                                                                                     Order
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidales
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Selenomonadales
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT   Clostridiales
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT   Clostridiales
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG   Clostridiales
##                                                                                                                                                                                                                                                    Family
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT  Bacteroidaceae
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  Prevotellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Veillonellaceae
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Ruminococcaceae
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Ruminococcaceae
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG Ruminococcaceae
##                                                                                                                                                                                                                                                      Genus
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT      Bacteroides
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT       Prevotella
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG         Dialister
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Faecalibacterium
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT     Ruminococcus
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG             <NA>
##                                                                                                                                                                                                                                               Species
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT        <NA>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT        <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG         <NA>
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT prausnitzii
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT      bromii
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG        <NA>
write.table(sigtab_dds.dds.d.9.broad, file="./results/deseq_d.9_broad_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file

# Quick check of factor levels
mcols(res.dds.d.9.broad, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
# Prepare to join results data.table and taxonomy table
resdt.dds.d.9.broad = data.table(as(results(dds.d.9.broad, cooksCutoff = FALSE), "data.frame"),
                   keep.rownames = TRUE)
setnames(resdt.dds.d.9.broad, "rn", "OTU")
taxdt.dds.d.9.com = data.table(data.frame(as(tax_table(ps1.d.9.broad), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d.9.com, "rn", "OTU")

# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d.9.com, "OTU")
setkeyv(resdt.dds.d.9.broad, "OTU")
resdt.dds.d.9.broad <- taxdt.dds.d.9.com[resdt.dds.d.9.broad]
resdt.dds.d.9.broad
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species baseMean
##    1:     Ruminococcaceae                 NA        NA  0.00000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum  0.00000
##    3:    Fusobacteriaceae      Fusobacterium        NA  0.00000
##    4:       Rikenellaceae                 NA        NA  0.00000
##    5:      Eubacteriaceae        Eubacterium        NA  0.00000
##   ---                                                          
## 1586:      Bacteroidaceae        Bacteroides stercoris  0.00000
## 1587:      Bacteroidaceae        Bacteroides        NA  0.00000
## 1588:      Prevotellaceae         Prevotella        NA  0.00000
## 1589:      Prevotellaceae         Prevotella     bivia  0.00000
## 1590: Methanobacteriaceae Methanobrevibacter        NA  2.02012
##       log2FoldChange    lfcSE       stat    pvalue      padj
##    1:             NA       NA         NA        NA        NA
##    2:             NA       NA         NA        NA        NA
##    3:             NA       NA         NA        NA        NA
##    4:             NA       NA         NA        NA        NA
##    5:             NA       NA         NA        NA        NA
##   ---                                                       
## 1586:             NA       NA         NA        NA        NA
## 1587:             NA       NA         NA        NA        NA
## 1588:             NA       NA         NA        NA        NA
## 1589:             NA       NA         NA        NA        NA
## 1590:      -3.688854 5.350637 -0.6894234 0.4905569 0.8381624
resdt.dds.d.9.broad[, Significant := padj < alpha]
resdt.dds.d.9.broad[!is.na(Significant)]
##                                                                                                                                                                                                                                             OTU
##   1:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTCGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   2:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGCTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   3:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCAGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   4:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   5:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAGCTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##  ---                                                                                                                                                                                                                                           
## 460:  TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATGTTAGGGCTCAACCCTGAAACTGCCTCTAATACTGTTGGACTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 461:  TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCAACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 462:  TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCAGGGGCTCAACCCCTGGATTGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 463:  TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 464: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##       Kingdom          Phylum            Class              Order
##   1: Bacteria      Firmicutes       Clostridia      Clostridiales
##   2: Bacteria      Firmicutes       Clostridia      Clostridiales
##   3: Bacteria      Firmicutes       Clostridia      Clostridiales
##   4: Bacteria      Firmicutes       Clostridia      Clostridiales
##   5: Bacteria      Firmicutes       Clostridia      Clostridiales
##  ---                                                             
## 460: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 461: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 462: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 463: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 464:  Archaea   Euryarchaeota  Methanobacteria Methanobacteriales
##                   Family              Genus     Species    baseMean
##   1:     Ruminococcaceae   Faecalibacterium          NA    6.867618
##   2:     Ruminococcaceae   Faecalibacterium          NA  254.644237
##   3:     Ruminococcaceae   Faecalibacterium          NA   53.497773
##   4:     Ruminococcaceae   Faecalibacterium prausnitzii 1720.798723
##   5:     Ruminococcaceae   Faecalibacterium          NA   21.346966
##  ---                                                               
## 460:       Rikenellaceae          Alistipes          NA    1.716905
## 461:       Rikenellaceae          Alistipes  putredinis  317.759626
## 462: Verrucomicrobiaceae        Akkermansia          NA  109.357806
## 463: Verrucomicrobiaceae        Akkermansia muciniphila   81.646341
## 464: Methanobacteriaceae Methanobrevibacter          NA    2.020120
##      log2FoldChange    lfcSE       stat       pvalue        padj
##   1:     -5.3882408 5.339579 -1.0091134 3.129202e-01 0.838162439
##   2:      6.1745647 4.930232  1.2523882 2.104284e-01 0.806932161
##   3:     11.0034829 3.561049  3.0899556 2.001864e-03 0.013461809
##   4:      1.8541965 1.551995  1.1947179 2.321973e-01 0.835190115
##   5:    -19.6078629 5.335357 -3.6750801 2.377748e-04 0.002839852
##  ---                                                            
## 460:     -3.4876899 5.351838 -0.6516807 5.146072e-01 0.838162439
## 461:     -0.9567253 2.675959 -0.3575261 7.206980e-01 0.860704433
## 462:    -21.8225414 5.333679 -4.0914612 4.286638e-05 0.001989000
## 463:     -0.5092594 4.931990 -0.1032564 9.177595e-01 0.952663104
## 464:     -3.6888541 5.350637 -0.6894234 4.905569e-01 0.838162439
##      Significant
##   1:       FALSE
##   2:       FALSE
##   3:        TRUE
##   4:       FALSE
##   5:        TRUE
##  ---            
## 460:       FALSE
## 461:       FALSE
## 462:        TRUE
## 463:       FALSE
## 464:       FALSE
resdt.dds.d.9.broad
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species baseMean
##    1:     Ruminococcaceae                 NA        NA  0.00000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum  0.00000
##    3:    Fusobacteriaceae      Fusobacterium        NA  0.00000
##    4:       Rikenellaceae                 NA        NA  0.00000
##    5:      Eubacteriaceae        Eubacterium        NA  0.00000
##   ---                                                          
## 1586:      Bacteroidaceae        Bacteroides stercoris  0.00000
## 1587:      Bacteroidaceae        Bacteroides        NA  0.00000
## 1588:      Prevotellaceae         Prevotella        NA  0.00000
## 1589:      Prevotellaceae         Prevotella     bivia  0.00000
## 1590: Methanobacteriaceae Methanobrevibacter        NA  2.02012
##       log2FoldChange    lfcSE       stat    pvalue      padj Significant
##    1:             NA       NA         NA        NA        NA          NA
##    2:             NA       NA         NA        NA        NA          NA
##    3:             NA       NA         NA        NA        NA          NA
##    4:             NA       NA         NA        NA        NA          NA
##    5:             NA       NA         NA        NA        NA          NA
##   ---                                                                   
## 1586:             NA       NA         NA        NA        NA          NA
## 1587:             NA       NA         NA        NA        NA          NA
## 1588:             NA       NA         NA        NA        NA          NA
## 1589:             NA       NA         NA        NA        NA          NA
## 1590:      -3.688854 5.350637 -0.6894234 0.4905569 0.8381624       FALSE
volcano.d.9.broad.shed = ggplot(
  data = resdt.dds.d.9.broad[!is.na(Significant)][(pvalue < 1)],
  mapping = aes(x = log2FoldChange,
                y = -log10(pvalue),
                color = Phylum,
                label = OTU, label1 = Genus)) +
  theme_bw() +
  geom_point() + 
  geom_point(data = resdt.dds.d.9.broad[(Significant)], size = 7, alpha = 0.7) + 
  # geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
  theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
  geom_hline(yintercept = -log10(alpha)) +
  ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay -9 Broad Spectrum Antibiotics ~ Shedding") +
  theme(axis.title = element_text(size=12)) +
  theme(axis.text = element_text(size=12)) +
  theme(legend.text = element_text(size=12)) +
  geom_vline(xintercept = 0, lty = 2)
volcano.d.9.broad.shed

summary(res.dds.d.9.broad)
## 
## out of 464 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 1, 0.22% 
## LFC < 0 (down)   : 76, 16% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 0, 0% 
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
mcols(res.dds.d.9.broad, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
ggplotly(volcano.d.9.broad.shed)

Shedding: Day 0 Narrow Spectrum Antibiotics

# Differential Abundance Testing
ds.d0.narrow.shed <- phyloseq_to_deseq2(ps1.d0.narrow, ~Shedding)

geoMeans.ds.d0.narrow.shed <- apply(counts(ds.d0.narrow.shed), 1, gm_mean)
ds.d0.narrow.shed <- estimateSizeFactors(ds.d0.narrow.shed, geoMeans = geoMeans.ds.d0.narrow.shed)

dds.d0.narrow.shed <- DESeq(ds.d0.narrow.shed, test="Wald", fitType="local", betaPrior = FALSE)

alpha = 0.05

# Tabulate and write results
res.dds.d0.narrow.shed = results(dds.d0.narrow.shed, cooksCutoff = FALSE)
sigtab_dds.dds.d0.narrow.shed = res.dds.d0.narrow.shed[which(res.dds.d0.narrow.shed$padj < alpha), ]
sigtab_dds.dds.d0.narrow.shed = cbind(as(sigtab_dds.dds.d0.narrow.shed, "data.frame"), as(tax_table(ps1.d0.narrow)[rownames(sigtab_dds.dds.d0.narrow.shed), ], "matrix"))
summary(res.dds.d0.narrow.shed)
## 
## out of 141 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 8, 5.7% 
## LFC < 0 (down)   : 6, 4.3% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 99, 70% 
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
head(sigtab_dds.dds.d0.narrow.shed)
##                                                                                                                                                                                                                                            baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 156.59134
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  139.68413
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 915.37064
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT  24.77274
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG   28.90231
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT   28.85293
##                                                                                                                                                                                                                                           log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT     -24.313898
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT      -24.169993
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC      28.834345
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT     -21.814995
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG      -22.030192
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT        8.770506
##                                                                                                                                                                                                                                              lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.102730
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  3.102746
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 3.051926
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT 3.103426
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG  3.103310
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  3.050965
##                                                                                                                                                                                                                                                stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT -7.836291
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  -7.789871
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC  9.447917
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT -7.029327
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG  -7.098935
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT   2.874666
##                                                                                                                                                                                                                                                 pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 4.640501e-15
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  6.707756e-15
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 3.456413e-21
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT 2.075325e-12
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG  1.257222e-12
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  4.044555e-03
##                                                                                                                                                                                                                                                   padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 2.996131e-13
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  2.996131e-13
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 4.631594e-19
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT 2.780936e-11
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG  1.871864e-11
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  4.169003e-02
##                                                                                                                                                                                                                                            Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Bacteria
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Bacteria
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG  Bacteria
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Bacteria
##                                                                                                                                                                                                                                                  Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT     Firmicutes
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Synergistetes
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT    Firmicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG     Firmicutes
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT     Firmicutes
##                                                                                                                                                                                                                                                   Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Negativicutes
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC   Synergistia
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT       Bacilli
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG  Negativicutes
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Negativicutes
##                                                                                                                                                                                                                                                     Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Selenomonadales
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC   Synergistales
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT Lactobacillales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG  Selenomonadales
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Selenomonadales
##                                                                                                                                                                                                                                                       Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT     Prevotellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Acidaminococcaceae
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC     Synergistaceae
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT   Lactobacillaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG     Veillonellaceae
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Acidaminococcaceae
##                                                                                                                                                                                                                                                           Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT            Prevotella
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT        Acidaminococcus
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC        Cloacibacillus
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT         Lactobacillus
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG            Veillonella
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  Phascolarctobacterium
##                                                                                                                                                                                                                                                 Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT         copri
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT           <NA>
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC     evryensis
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT       ruminis
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG           <NA>
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT  succinatutens
write.table(sigtab_dds.dds.d0.narrow.shed, file="./results/deseq_d0_narrow_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file

# Quick check of factor levels
mcols(res.dds.d0.narrow.shed, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
# Prepare to join results data.table and taxonomy table
resdt.dds.d0.narrow.shed = data.table(as(results(dds.d0.narrow.shed, cooksCutoff = FALSE), "data.frame"),
                   keep.rownames = TRUE)
setnames(resdt.dds.d0.narrow.shed, "rn", "OTU")
taxdt.dds.d0.com = data.table(data.frame(as(tax_table(ps1.d0.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d0.com, "rn", "OTU")

# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d0.com, "OTU")
setkeyv(resdt.dds.d0.narrow.shed, "OTU")
resdt.dds.d0.narrow.shed <- taxdt.dds.d0.com[resdt.dds.d0.narrow.shed]
resdt.dds.d0.narrow.shed
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA 0.0000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum 0.0000000
##    3:    Fusobacteriaceae      Fusobacterium        NA 0.3496783
##    4:       Rikenellaceae                 NA        NA 0.0000000
##    5:      Eubacteriaceae        Eubacterium        NA 0.0000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris 0.0000000
## 1587:      Bacteroidaceae        Bacteroides        NA 0.0000000
## 1588:      Prevotellaceae         Prevotella        NA 0.0000000
## 1589:      Prevotellaceae         Prevotella     bivia 0.7704382
## 1590: Methanobacteriaceae Methanobrevibacter        NA 7.1099698
##       log2FoldChange    lfcSE       stat    pvalue      padj
##    1:             NA       NA         NA        NA        NA
##    2:             NA       NA         NA        NA        NA
##    3:     -0.8529424 3.153197 -0.2705008 0.7867750 0.9486504
##    4:             NA       NA         NA        NA        NA
##    5:             NA       NA         NA        NA        NA
##   ---                                                       
## 1586:             NA       NA         NA        NA        NA
## 1587:             NA       NA         NA        NA        NA
## 1588:             NA       NA         NA        NA        NA
## 1589:     -1.9021978 3.128970 -0.6079309 0.5432333 0.9486504
## 1590:      2.9627185 2.991595  0.9903473 0.3220044 0.9458676
resdt.dds.d0.narrow.shed[, Significant := padj < alpha]
resdt.dds.d0.narrow.shed[!is.na(Significant)]
##                                                                                                                                                                                                                                             OTU
##   1:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##   2:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   3:  ACAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGCGTAGGCGGACTGTCAAGTCAGTCGTGAAATACCGGGGCTTAACCCCGGGGCTGCGATTGAAACTGACAGCCTTGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGTGTGGGG
##   4:  CCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGACGGTTATTTAAGTCTGAAGTGAAAGCCCTCAGCTCAACTGAGGAATGGCTTTGGAAACTGGATGACTTGAGTGCAGTAGAGGAAAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGTTGAGGCTCGAAAGTGTGGGT
##   5:   CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGATTGTTAAGTCAGCGGTTAAAGGGTGTGGCTCAACCATGCATTGCCGTTGAAACTGGCGATCTTGAGTGCAGACAGGGATGCCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATCGCGAAGGCAGGTGTCCGGGCTGCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##  ---                                                                                                                                                                                                                                           
## 130:   GCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTTAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGAGGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTAGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGG
## 131:   GCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGTGGTTTCTTAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGGAAACTTGAGTGCAGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTAGCGAAGGCGGCTTTCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGG
## 132:  TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 133:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 134: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##       Kingdom          Phylum            Class              Order
##   1: Bacteria    Fusobacteria    Fusobacteriia    Fusobacteriales
##   2: Bacteria      Firmicutes       Clostridia      Clostridiales
##   3: Bacteria      Firmicutes       Clostridia      Clostridiales
##   4: Bacteria      Firmicutes          Bacilli    Lactobacillales
##   5: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
##  ---                                                             
## 130: Bacteria      Firmicutes       Clostridia      Clostridiales
## 131: Bacteria      Firmicutes       Clostridia      Clostridiales
## 132: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 133: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 134:  Archaea   Euryarchaeota  Methanobacteria Methanobacteriales
##                     Family              Genus     Species     baseMean
##   1:      Fusobacteriaceae      Fusobacterium          NA    0.3496783
##   2:       Ruminococcaceae   Faecalibacterium prausnitzii    3.1347101
##   3:       Ruminococcaceae                 NA          NA    0.1861645
##   4:      Leuconostocaceae          Weissella          NA    0.5050118
##   5:        Prevotellaceae     Paraprevotella          NA    0.3705344
##  ---                                                                  
## 130: Peptostreptococcaceae    Intestinibacter  bartlettii    1.0239045
## 131: Peptostreptococcaceae   Terrisporobacter          NA    1.9173003
## 132:   Verrucomicrobiaceae        Akkermansia muciniphila 1514.3149871
## 133:        Prevotellaceae         Prevotella       bivia    0.7704382
## 134:   Methanobacteriaceae Methanobrevibacter          NA    7.1099698
##      log2FoldChange    lfcSE       stat     pvalue      padj Significant
##   1:     -0.8529424 3.153197 -0.2705008 0.78677498 0.9486504       FALSE
##   2:      3.6439035 3.037194  1.1997599 0.23023260 0.7712792       FALSE
##   3:      2.4578628 3.180233  0.7728561 0.43960753 0.9486504       FALSE
##   4:     -1.3169564 3.141858 -0.4191649 0.67509563 0.9486504       FALSE
##   5:     -0.4681159 3.162862 -0.1480039 0.88233968 0.9486504       FALSE
##  ---                                                                    
## 130:      4.4155072 3.098948  1.4248406 0.15420329 0.6302357       FALSE
## 131:      5.3064398 3.077400  1.7243257 0.08464906 0.4616041       FALSE
## 132:     -0.7327842 2.965545 -0.2470994 0.80483132 0.9486504       FALSE
## 133:     -1.9021978 3.128970 -0.6079309 0.54323332 0.9486504       FALSE
## 134:      2.9627185 2.991595  0.9903473 0.32200440 0.9458676       FALSE
resdt.dds.d0.narrow.shed
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA 0.0000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum 0.0000000
##    3:    Fusobacteriaceae      Fusobacterium        NA 0.3496783
##    4:       Rikenellaceae                 NA        NA 0.0000000
##    5:      Eubacteriaceae        Eubacterium        NA 0.0000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris 0.0000000
## 1587:      Bacteroidaceae        Bacteroides        NA 0.0000000
## 1588:      Prevotellaceae         Prevotella        NA 0.0000000
## 1589:      Prevotellaceae         Prevotella     bivia 0.7704382
## 1590: Methanobacteriaceae Methanobrevibacter        NA 7.1099698
##       log2FoldChange    lfcSE       stat    pvalue      padj Significant
##    1:             NA       NA         NA        NA        NA          NA
##    2:             NA       NA         NA        NA        NA          NA
##    3:     -0.8529424 3.153197 -0.2705008 0.7867750 0.9486504       FALSE
##    4:             NA       NA         NA        NA        NA          NA
##    5:             NA       NA         NA        NA        NA          NA
##   ---                                                                   
## 1586:             NA       NA         NA        NA        NA          NA
## 1587:             NA       NA         NA        NA        NA          NA
## 1588:             NA       NA         NA        NA        NA          NA
## 1589:     -1.9021978 3.128970 -0.6079309 0.5432333 0.9486504       FALSE
## 1590:      2.9627185 2.991595  0.9903473 0.3220044 0.9458676       FALSE
volcano.d0.narrow.shed = ggplot(
  data = resdt.dds.d0.narrow.shed[!is.na(Significant)][(pvalue < 1)],
  mapping = aes(x = log2FoldChange,
                y = -log10(pvalue),
                color = Phylum,
                label = OTU, label1 = Genus)) +
  theme_bw() +
  geom_point() + 
  geom_point(data = resdt.dds.d0.narrow.shed[(Significant)], size = 7, alpha = 0.7) + 
  # geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
  theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
  geom_hline(yintercept = -log10(alpha)) +
  ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 0 Narrow Spectrum Antibiotics ~ Shedding") +
  theme(axis.title = element_text(size=12)) +
  theme(axis.text = element_text(size=12)) +
  theme(legend.text = element_text(size=12)) +
  geom_vline(xintercept = 0, lty = 2)
volcano.d0.narrow.shed

summary(res.dds.d0.narrow.shed)
## 
## out of 141 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 8, 5.7% 
## LFC < 0 (down)   : 6, 4.3% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 99, 70% 
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
mcols(res.dds.d0.narrow.shed, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
ggplotly(volcano.d0.narrow.shed)

Shedding: Day 0 Broad Spectrum Antibiotics

sample_data(ps1)$day
##   [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
##  [24] -9  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7
##  [47]  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  0  0  0
##  [70]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [93]  0  0  0  0  0  0  0  0
ps1.d0.broad <- subset_samples(ps1.broad, day == "0")
sample_data(ps1.d0.broad)$day
##  [1] 0 0 0 0 0 0 0 0 0 0
## Levels: 0
sample_data(ps1.d0.broad)$randomization_arm
##  [1] Broad spectrum antibiotics Broad spectrum antibiotics
##  [3] Broad spectrum antibiotics Broad spectrum antibiotics
##  [5] Broad spectrum antibiotics Broad spectrum antibiotics
##  [7] Broad spectrum antibiotics Broad spectrum antibiotics
##  [9] Broad spectrum antibiotics Broad spectrum antibiotics
## Levels: Broad spectrum antibiotics
# Differential Abundance Testing
ds.d0.broad <- phyloseq_to_deseq2(ps1.d0.broad, ~Shedding)

geoMeans.ds.d0.broad <- apply(counts(ds.d0.broad), 1, gm_mean)
ds.d0.broad <- estimateSizeFactors(ds.d0.broad, geoMeans = geoMeans.ds.d0.broad)

dds.d0.broad <- DESeq(ds.d0.broad, test="Wald", fitType="local", betaPrior = FALSE)

alpha = 0.05

# Tabulate and write results
res.dds.d0.broad = results(dds.d0.broad, cooksCutoff = FALSE)
sigtab_dds.dds.d0.broad = res.dds.d0.broad[which(res.dds.d0.broad$padj < alpha), ]
sigtab_dds.dds.d0.broad = cbind(as(sigtab_dds.dds.d0.broad, "data.frame"), as(tax_table(ps1.d0.broad)[rownames(sigtab_dds.dds.d0.broad), ], "matrix"))
summary(res.dds.d0.broad)
## 
## out of 88 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 0, 0% 
## LFC < 0 (down)   : 1, 1.1% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 34, 39% 
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
head(sigtab_dds.dds.d0.broad)
##                                                                                                                                                                                                                                           baseMean
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT 245.1928
##                                                                                                                                                                                                                                           log2FoldChange
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT      -23.83235
##                                                                                                                                                                                                                                              lfcSE
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT 3.884625
##                                                                                                                                                                                                                                                stat
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT -6.135045
##                                                                                                                                                                                                                                                 pvalue
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT 8.513503e-10
##                                                                                                                                                                                                                                                   padj
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT 7.491883e-08
##                                                                                                                                                                                                                                            Kingdom
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Bacteria
##                                                                                                                                                                                                                                               Phylum
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Firmicutes
##                                                                                                                                                                                                                                             Class
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Bacilli
##                                                                                                                                                                                                                                                     Order
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Lactobacillales
##                                                                                                                                                                                                                                                     Family
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Lactobacillaceae
##                                                                                                                                                                                                                                                 Genus
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Pediococcus
##                                                                                                                                                                                                                                           Species
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT    <NA>
write.table(sigtab_dds.dds.d0.broad, file="./results/deseq_d0_broad_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file

# Quick check of factor levels
mcols(res.dds.d0.broad, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
# Prepare to join results data.table and taxonomy table
resdt.dds.d0.broad = data.table(as(results(dds.d0.broad, cooksCutoff = FALSE), "data.frame"),
                   keep.rownames = TRUE)
setnames(resdt.dds.d0.broad, "rn", "OTU")
taxdt.dds.d0.com = data.table(data.frame(as(tax_table(ps1.d0.broad), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d0.com, "rn", "OTU")

# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d0.com, "OTU")
setkeyv(resdt.dds.d0.broad, "OTU")
resdt.dds.d0.broad <- taxdt.dds.d0.com[resdt.dds.d0.broad]
resdt.dds.d0.broad
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species baseMean
##    1:     Ruminococcaceae                 NA        NA        0
##    2:    Fusobacteriaceae      Fusobacterium nucleatum        0
##    3:    Fusobacteriaceae      Fusobacterium        NA        0
##    4:       Rikenellaceae                 NA        NA        0
##    5:      Eubacteriaceae        Eubacterium        NA        0
##   ---                                                          
## 1586:      Bacteroidaceae        Bacteroides stercoris        0
## 1587:      Bacteroidaceae        Bacteroides        NA        0
## 1588:      Prevotellaceae         Prevotella        NA        0
## 1589:      Prevotellaceae         Prevotella     bivia        0
## 1590: Methanobacteriaceae Methanobrevibacter        NA        0
##       log2FoldChange lfcSE stat pvalue padj
##    1:             NA    NA   NA     NA   NA
##    2:             NA    NA   NA     NA   NA
##    3:             NA    NA   NA     NA   NA
##    4:             NA    NA   NA     NA   NA
##    5:             NA    NA   NA     NA   NA
##   ---                                      
## 1586:             NA    NA   NA     NA   NA
## 1587:             NA    NA   NA     NA   NA
## 1588:             NA    NA   NA     NA   NA
## 1589:             NA    NA   NA     NA   NA
## 1590:             NA    NA   NA     NA   NA
resdt.dds.d0.broad[, Significant := padj < alpha]
resdt.dds.d0.broad[!is.na(Significant)]
##                                                                                                                                                                                                                                               OTU
##  1:     ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##  2:     ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##  3:     CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGCCCCTTAAGCGTGTTGTGAAATGCCGCGGCTCAACCGTGGCACTGCAGCGCGAACTGGGGGGCTTGAGTGCACGCAACGCAGGTGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTGCGGGAGTGCGACTGACGCTGAAGCTCGAAGGTGCGGGT
##  4:     CCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGACGGTTCGATAAGTCTGAAGTGAAAGCCCACAGCTCAACTGTGGAATGGCTTTGGAAACTGTCGAACTTGAGTGCAGTAGAGGTAAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTTACTGGACTGCAACTGACGTTGAGGCTCGAAAGTGTGGGT
##  5:     CCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGACGGTTGATTAAGTCTGATGTGAAAGCCCGGAGCTCAACTCCGGAAAGGCATTGGAAACTGGTCAACTTGAGTGCAGTAGAGGTAAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGCGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGTGTGGGT
##  6:      CCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGG
##  7:     CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT
##  8:     CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAATTGATACTGGCAGTCTTGAGTACAGTTGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTAACCTGTAACTGACATTGATGCTCGAAAGTGTGGGT
##  9:     CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCTGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGT
## 10:     CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT
## 11:      CCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTGATAAGTCTGAAGTTAAAGGCTGTGGCTCAACCATAGTTCGCTTTGGAAACTGTCAAACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGG
## 12:      CCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGTGGTTTATTAAGTCTGGTGTAAAAGGCAGTGGCTCAACCATTGTATGCATTGGAAACTGGTAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCCTGTAACTGACACTGAGGCTCGAAAGCGTGGGG
## 13:     CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 14:     CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACGATAACTGACGGTGAGGCGCGAAAGTGTGGGG
## 15:     CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 16:     CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGTGGCTCAACCTCTGCACTGCAGCGCGAACTGGTCTTCTTGAGTACGCACAACGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACGGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 17:     CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTCTTATAAGCGTGTTGTGAAATGTCGGGGCTCAACCTGGGCATTGCAGCGCGAACTGTGAGGCTTGAGTGCGCAGGAAGTAGGCGGAATTCGTCGTGTAGCGGTGAAATGCTTAGATATGACGAAGAACTCCGATTGCGAAGGCAGCCTGCTGTAGCGCAACTGACGCTGAAGCTCGAAAGCGTGGGT
## 18:     GCAAGCGTTAATCGGAATCACTGGGCGTAAAGCGCACGTAGGCGGCTTGGTAAGTCAGGGGTGAAATCCCACAGCCCAACTGTGGAACTGCCTTTGATACTGCCAGGCTTGAGTACCGGAGAGGGTGGCGGAATTCCAGGTGTAGGAGTGAAATCCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCCACCTGGACGGTAACTGACGCTGAGGTGCGAAAGCGTGGGT
## 19:     GCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTGGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGG
## 20:     GCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGG
## 21:     GCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTCGCTAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAACTGCATTTGTGACTGGCGGGCTAGAGTATGGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGCCAATACTGACGCTCATGCACGAAAGCGTGGGG
## 22:     GCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTCGTAAGATAGATGTGAAATCCCCGGGCTCAACCTGGGAATTGCATTTATGACTGCGGGACTGGAGTTTGTCAGAGGGGGGTGGAATTCCAAGTGTAGCAGTGAAATGCGTAGATATTTGGAAGAACACCGATGGCGAAGGCAGCCCCCTGGGACATGACTGACGCTCATGCACGAAAGCGTGGGG
## 23:      GCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGGGAGCAGGCGGCAGCAAGGGTCTGTGGTGAAAGCCTGAAGCTTAACTTCAGTAAGCCATAGAAACCAGGCAGCTAGAGTGCAGGAGAGGATCGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGACGATCTGGCCTGCAACTGACGCTCAGTCCCGAAAGCGTGGGG
## 24:     GCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGG
## 25:     GCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGG
## 26:     GCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGG
## 27:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGGACTGCAAGTTGGATGTGAAATACCGTGGCTTAACCACGGAACTGCATCCAAAACTGTAGTTCTTGAGTGAAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTTTAACTGACGCTGAGGCTCGAAAGTGTGGGG
## 28:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGTCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATAACTGACGCTGAGGCTCGAAAGCGTGGGG
## 29:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAAGGCAAGTCTGAAGTGAAAGCCCGGTGCTTAACGCCGGGACTGCTTTGGAAACTGTTTGGCTGGAGTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG
## 30:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCGAAGCAAGTCTGAAGTGAAAGCCCGGGGCTTAACCCCGGGACTGCTTTGGAAACTGTTTTGCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGG
## 31:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCTGTGCAAGTCTGAAGTGAAAGGCATGGGCTCAACCTGTGGACTGCTTTGGAAACTGTGCAGCTAGAGTGTCGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG
## 32:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTAAAGCAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTTTAACTAGAGTGCTGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGG
## 33:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCCAGGCAAGTCAGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTTGAAACTGCAGGGCTAGAGTGCAGGAGGGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGG
## 34:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCCATGCAAGTCAGAAGTGAAAATCCGGGGCTCAACCCCGGAACTGCTTTTGAAACTGTAAGGCTGGAGTGCAGGAGGGGTGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTCACTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGG
## 35:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCTGCGCAAGTCAGGAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTCTTGAAACTGCGCGGCTTGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGG
## 36:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGATTGCAAGTCAGATGTGAAAACTGGGGGCTCAACCTCCAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGG
## 37:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGTGGGACTACAAGTCAGGTGTGAAAACCAGGGGCTCAACCTCTGGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGG
## 38:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGTGGCAAGGCAAGTCTGAAGTGAAAATCCGGGGCTCAACCCCGGAACTGCTTTGGAAACTGTTTAGCTGGAGTACAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGACTTACTGGACTGCTACTGACACTGAGGCACGAAAGCGTGGGG
## 39:     GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGTGGTGAGACAAGTCTGAAGTGAAAATCCGGGGCTTAACCCCGGAACTGCTTTGGAAACTGCCTGACTAGAGTACAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGACTTACTGGACTGCTACTGACACTGAGGCACGAAAGCGTGGGG
## 40:     GCAAGCGTTATCCGGATTTATTGGGCGTAAAGAGAGTGCAGGCGGTTTTCTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGAAGTGCATCGGAAACTGGATAACTTGAGTGCAGAAGAGGGTAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTACCTGGTCTGCAACTGACGCTGAGACTCGAAAGCATGGGT
## 41:     GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT
## 42:     GCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGACAGCAAGTTGGATGTGAAATACCGAGGCTTAACCACGGAGCTGCATCCAAAACTGTTGTTCTTGAGTGAAGTAGAGGTAGGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCTTTAACTGACGCTGAGGCTCGAAAGTGTGGGG
## 43:      GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT
## 44:      GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATCAGTCAGTCTGTCTTAAAAGTTCGGGGCTTAACCCCGTGATGGGATGGAAACTGCTGATCTAGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACGAAAACTGACGCTGAGGCGCGAAAGCCAGGGG
## 45:      GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG
## 46:     GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTAATAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGTTAAACTTGAGTGCAGGAGAGAAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTTTGGCCTGTAACTGACACTGAGGCGCGAAAGCGTGGGG
## 47:      GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT
## 48:      GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCGCGCAGGCGGCGTCGTAAGTCGGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGACCGAAACTGCGATGCTAGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAAGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG
## 49:     GCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGATTTTTAAGTGAGATGTGAAATACCCGGGCTTAACTTGGGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAAGGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGCTTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGG
## 50:     GCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGTGGATATTTAAGTGGGATGTGAAATACTCGGGCTTAACCTGGGTGCTGCATTCCAAACTGGATATCTAGAGTGCAGGAGAGGAAAGTAGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAATACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGG
## 51:     GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGCAGCCGGGTCTGCAAGTCAGATGTGAAATCCATGGGCTCAACCCATGAACTGCATTTGAAACTGTAGATCTTGAGTGTCGGAGGGGCAATCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACGATAACTGACGGTGAGGCGCGAAAGTGTGGGG
## 52:     GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGCCGGGAGGGCAAGTCAGATGTGAAATCCACGGGCTCAACTCGTGAACTGCATTTGAAACTACTCTTCTTGAGTATCGGAGAGGCAATCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACGACAACTGACGGTGAGGCGCGAAAGCGTGGGG
## 53:     GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGATTGGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTTGAAACTGTTAGTCTTGAGTGAAGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCTTTAACTGACGCTGAGGCACGAAAGTGTGGGT
## 54:     GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT
## 55:     GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAGAATAAGTCTGATGTGAAAGCCCTCGGCTTAACCGAGGAACTGCATCGGAAACTGTTTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT
## 56:     GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAATGATAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAACTGCATCGGAAACTGTCATTCTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT
## 57:     GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAGAAATAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAACTGCATCGGAAACTGTTTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT
## 58:     GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGG
## 59:     GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGT
## 60:     GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGAAGTGCATCGGAAACCAGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGT
## 61:     GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTTTTAAGTCTGATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGTATGGGT
## 62:     GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT
## 63:      GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGCGGTTTGTTGCGTCTGGTGTGAAAGCTTACTGCTTAACGGTAGGTTGCGCTGGATACGGGCAGGCTTGAGTGCAGTAGGGGAGACTGGAATTCTCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCTATGGCGAAGGCAGGTCTCTGGGCTGTTACTGACGCTGAGGAGCGAAAGCGTGGGG
## 64:     GCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTGGGTAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAACTGCATTTGTGACTGTCCGACTGGAGTATGTCAGAGGGGGGTGGAATTCCAAGTGTAGCAGTGAAATGCGTAGATATTTGGAAGAACACCGATGGCGAAGGCAGCCCCCTGGGGCAAAACTGACGCTCATGCACGAAAGCGTGGGG
## 65:     GCGAGCGTTAATCGGAATTACTGGGCGTAAAGGGTGCGCAGGCGGTTGAGTAAGACAGATGTGAAATCCCCGAGCTTAACTCGGGAATGGCATATGTGACTGCTCGACTAGAGTGTGTCAGAGGGAGGTGGAATTCCACGTGTAGCAGTGAAATGCGTAGATATGTGGAAGAACACCGATGGCGAAGGCAGCCTCCTGGGACATAACTGACGCTCAGGCACGAAAGCGTGGGG
## 66:     GCGAGCGTTATCCGGAATGATTGGGCGTAAAGGGTGCGTAGGTGGCAGATCAAGTCTGGAGTAAAAGGTATGGGCTCAACCCGTACTGGCTCTGGAAACTGATCAGCTAGAGAACAGAAGAGGACGGCGGAACTCCATGTGTAGCGGTAAAATGCGTAGATATATGGAAGAACACCGGTGGCGAAGGCGGCCGTCTGGTCTGGATTCTGACACTGAAGCACGAAAGCGTGGGG
## 67:      GCGAGCGTTATCCGGAATTATTGGGCGTAAAGAGGGAGCAGGCGGCACTAAGGGTCTGTGGTGAAAGATCGAAGCTTAACTTCGGTAAGCCATGGAAACCGTAGAGCTAGAGTGTGTGAGAGGATCGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGACGATCTGGCGCATAACTGACGCTCAGTCCCGAAAGCGTGGGG
## 68:     GCGAGCGTTATCCGGATTTACTGGGCGTAAAGGATGCGTAGGTGGAATTTTAAGTGGGATGTGAAATACCCGGGCTCAACCTGGGAACTGCATTCCAAACTGGAATTCTAGAGTGCAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACACTGAGGCATGAAAGCGTGGGG
## 69:     GCGAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGTAGGCGGGAATGCAAGTCAGATGTGAAATCCAGGGGCTTAACCCTTGAACTGCATTTGAAACTGTATTTCTTGAGTGTCGGAGAGGTTGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCAACTGGACGATAACTGACGCTGAGGCGCGAAAGCGTGGGG
## 70:     GCGAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGTTTGTTAAGTCAGAAGTGAAATTTAGGGGCTCAACCTCTAAGCTGCTTCTGAAACTGATGAACTAGAGTGTGGGAGAGGAAAGTGGAATTCCGAGTGTAGCGGTGAAATGCGTAGAGATTCGGAGGAACACCAGTAGCGAAGGCGGCTTTCTGGACCATAACTGACGCTGAGGCACGAAAGCGTGGGG
## 71:     GCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGCAGACGGGAGATTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTTTCCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACCCCGATTGCGAAGGCAGCTTGCTAAACTGTAACTGACGTTCATGCTCGAAAGTGTGGGT
## 72:     GCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGCAGACGGGGGATTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTTCCCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAAGAACCCCGATTGCGAAGGCAGCCTGCTAAGCTGTAACTGACGTTGAGGCTCGAAAGTGTGGGT
## 73:     GCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCAAGGTAAGTCAGCGGTGAAAGACCAGGGCTCAACTCTGGAAGTGCCGTTGATACTGTCTGGCTAGAATGATTCCGCCGTGGGAGGAATGAGTAGTGTAGCGGTGAAATGCATAGATATTACTCAGAACACCGATTGCGAAGGCATCTCACGAGGGGTTCATTGACGCTGAGGCACGAAAGCGTGGGG
## 74:     GCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCACGCCAAGTCAGCGGTGAAATTTTCGGGCTCAACCCGGACTGTGCCGTTGAAACTGGCGAGCTAGAGTGCACAAGAGGCAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTGCTAGGGTGCGACAGACGCTGAGGCACGAAAGCGTGGGT
## 75:     GCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTGGTGATTTAAGTCAGCGGTGAAAGTTTGTGGCTCAACCATAAAATTGCCGTTGAAACTGGGTTACTTGAGTGTGTTTGAGGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCTTACTAAACCATAACTGACACTGAAGCACGAAAGCGTGGGG
## 76:     GCGAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGTAGGCGGGACGGCAAGTCAGATGTGAAAACTATGGGCTCAACCCATAGACTGCATTTGAAACTGTTGTTCTTGAGTGAGGTAGAGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGAGATCAGGAGGAACATCGGTGGCGAAGGCGGCTTACTGGGCCTTTACTGACGCTGAGGCTCGAAAGCGTGGGT
## 77:    GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTTGTAGGCGGTTTGTCGCGTCTGCTGTGAAAGGCCGGAGCTTAACTCCGTGTATTGCAGTGGGTACGGGCAGACTAGAGTGCAGTAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCTGTAACTGACGCTGAGAAGCGAAAGCATGGGG
## 78:    GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTTGTAGGCGGTTTGTCGCGTCTGCTGTGAAAGGCCGGGGCTTAACCCCGTGTATTGCAGTGGGTACGGGCAGACTAGAGTGCAGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGATGGCGAAGGCAGGTCTCTGGGCTGTAACTGACGCTGAGAAGCGAAAGCATGGGG
## 79:    GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTTGTAGGCGGTTTGTCGCGTCTGCTGTGAAAGGCCGGGGCTTAACTCCGTGTATTGCAGTGGGTACGGGCAGACTAGAGTGCAGTAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCTGTAACTGACGCTGAGAAGCGAAAGCATGGGG
## 80:      GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAGGTAAGTCTATCTTAAAAGTGCGGGGCTCAACCCCGTGAGGGGATGGAAACTATCTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGG
## 81:     GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGG
## 82:     GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTTGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCAGGCTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGG
## 83:     GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT
## 84:     GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC
## 85: GCGGTAACACAAAGAGGGCGAGCGTTAATCATAATGGTTTAAAGGATCCGTAGAATGAATTATATATTATAATTTAGAGTTAATAAAATTAATTAAAGAATTATAATAGTAAAGATGAAATAATAATAATAATTATAAGACTAATATATGTGAAAATATTAATTAAATATTAACTGACATTGAGGGATTAAAACTAGAGTAGCGAAACGGATTAGAAACCCGTGTAGTCCGGCTGAC
## 86:      GCTAGCGTTATCCGGAATTACTGGGCGTAAAGGGTGCGTAGGTGGTTTCTTAAGTCAGAGGTGAAAGGCTACGGCTCAACCGTAGTAAGCCTTTGAAACTGGGAAACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGG
## 87:      GCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTTAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGAGGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTAGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGG
## 88:     TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
##                                                                                                                                                                                                                                               OTU
##      Kingdom          Phylum               Class
##  1: Bacteria      Firmicutes          Clostridia
##  2: Bacteria      Firmicutes          Clostridia
##  3: Bacteria   Bacteroidetes         Bacteroidia
##  4: Bacteria      Firmicutes             Bacilli
##  5: Bacteria      Firmicutes             Bacilli
##  6: Bacteria      Firmicutes             Bacilli
##  7: Bacteria   Bacteroidetes         Bacteroidia
##  8: Bacteria   Bacteroidetes         Bacteroidia
##  9: Bacteria   Bacteroidetes         Bacteroidia
## 10: Bacteria   Bacteroidetes         Bacteroidia
## 11: Bacteria      Firmicutes             Bacilli
## 12: Bacteria      Firmicutes             Bacilli
## 13: Bacteria   Bacteroidetes         Bacteroidia
## 14: Bacteria   Bacteroidetes         Bacteroidia
## 15: Bacteria   Bacteroidetes         Bacteroidia
## 16: Bacteria   Bacteroidetes         Bacteroidia
## 17: Bacteria   Bacteroidetes         Bacteroidia
## 18: Bacteria  Proteobacteria Deltaproteobacteria
## 19: Bacteria  Proteobacteria Gammaproteobacteria
## 20: Bacteria  Proteobacteria Gammaproteobacteria
## 21: Bacteria  Proteobacteria  Betaproteobacteria
## 22: Bacteria  Proteobacteria  Betaproteobacteria
## 23: Bacteria      Firmicutes    Erysipelotrichia
## 24: Bacteria      Firmicutes             Bacilli
## 25: Bacteria  Actinobacteria      Actinobacteria
## 26: Bacteria  Actinobacteria      Actinobacteria
## 27: Bacteria      Firmicutes          Clostridia
## 28: Bacteria      Firmicutes          Clostridia
## 29: Bacteria      Firmicutes          Clostridia
## 30: Bacteria      Firmicutes          Clostridia
## 31: Bacteria      Firmicutes          Clostridia
## 32: Bacteria      Firmicutes          Clostridia
## 33: Bacteria      Firmicutes          Clostridia
## 34: Bacteria      Firmicutes          Clostridia
## 35: Bacteria      Firmicutes          Clostridia
## 36: Bacteria      Firmicutes          Clostridia
## 37: Bacteria      Firmicutes          Clostridia
## 38: Bacteria      Firmicutes          Clostridia
## 39: Bacteria      Firmicutes          Clostridia
## 40: Bacteria      Firmicutes             Bacilli
## 41: Bacteria      Firmicutes             Bacilli
## 42: Bacteria      Firmicutes          Clostridia
## 43: Bacteria      Firmicutes       Negativicutes
## 44: Bacteria      Firmicutes       Negativicutes
## 45: Bacteria      Firmicutes       Negativicutes
## 46: Bacteria      Firmicutes             Bacilli
## 47: Bacteria      Firmicutes       Negativicutes
## 48: Bacteria      Firmicutes       Negativicutes
## 49: Bacteria      Firmicutes          Clostridia
## 50: Bacteria      Firmicutes          Clostridia
## 51: Bacteria      Firmicutes          Clostridia
## 52: Bacteria      Firmicutes          Clostridia
## 53: Bacteria      Firmicutes          Clostridia
## 54: Bacteria      Firmicutes          Clostridia
## 55: Bacteria      Firmicutes             Bacilli
## 56: Bacteria      Firmicutes             Bacilli
## 57: Bacteria      Firmicutes             Bacilli
## 58: Bacteria      Firmicutes             Bacilli
## 59: Bacteria      Firmicutes             Bacilli
## 60: Bacteria      Firmicutes             Bacilli
## 61: Bacteria      Firmicutes             Bacilli
## 62: Bacteria      Firmicutes             Bacilli
## 63: Bacteria  Actinobacteria      Actinobacteria
## 64: Bacteria  Proteobacteria  Betaproteobacteria
## 65: Bacteria  Proteobacteria  Betaproteobacteria
## 66: Bacteria      Firmicutes    Erysipelotrichia
## 67: Bacteria      Firmicutes    Erysipelotrichia
## 68: Bacteria      Firmicutes          Clostridia
## 69: Bacteria      Firmicutes          Clostridia
## 70: Bacteria      Firmicutes          Clostridia
## 71: Bacteria   Bacteroidetes         Bacteroidia
## 72: Bacteria   Bacteroidetes         Bacteroidia
## 73: Bacteria   Bacteroidetes         Bacteroidia
## 74: Bacteria   Bacteroidetes         Bacteroidia
## 75: Bacteria   Bacteroidetes         Bacteroidia
## 76: Bacteria      Firmicutes          Clostridia
## 77: Bacteria  Actinobacteria      Actinobacteria
## 78: Bacteria  Actinobacteria      Actinobacteria
## 79: Bacteria  Actinobacteria      Actinobacteria
## 80: Bacteria      Firmicutes       Negativicutes
## 81: Bacteria  Actinobacteria      Actinobacteria
## 82: Bacteria  Actinobacteria      Actinobacteria
## 83: Bacteria      Firmicutes             Bacilli
## 84: Bacteria   Synergistetes         Synergistia
## 85: Bacteria  Proteobacteria Gammaproteobacteria
## 86: Bacteria      Firmicutes          Clostridia
## 87: Bacteria      Firmicutes          Clostridia
## 88: Bacteria Verrucomicrobia    Verrucomicrobiae
##      Kingdom          Phylum               Class
##                                  Order                       Family
##  1:                      Clostridiales              Ruminococcaceae
##  2:                      Clostridiales              Ruminococcaceae
##  3:                      Bacteroidales               Prevotellaceae
##  4:                    Lactobacillales             Leuconostocaceae
##  5:                    Lactobacillales             Leuconostocaceae
##  6:                    Lactobacillales             Streptococcaceae
##  7:                      Bacteroidales               Bacteroidaceae
##  8:                      Bacteroidales               Bacteroidaceae
##  9:                      Bacteroidales               Bacteroidaceae
## 10:                      Bacteroidales               Bacteroidaceae
## 11:                    Lactobacillales             Streptococcaceae
## 12:                    Lactobacillales             Streptococcaceae
## 13:                      Bacteroidales               Prevotellaceae
## 14:                      Bacteroidales               Prevotellaceae
## 15:                      Bacteroidales               Prevotellaceae
## 16:                      Bacteroidales               Prevotellaceae
## 17:                      Bacteroidales               Prevotellaceae
## 18:                 Desulfovibrionales          Desulfovibrionaceae
## 19:                  Enterobacteriales           Enterobacteriaceae
## 20:                  Enterobacteriales           Enterobacteriaceae
## 21:                    Burkholderiales             Burkholderiaceae
## 22:                    Burkholderiales               Sutterellaceae
## 23:                 Erysipelotrichales          Erysipelotrichaceae
## 24:                         Bacillales                Bacillaceae_1
## 25:                  Bifidobacteriales           Bifidobacteriaceae
## 26:                  Bifidobacteriales           Bifidobacteriaceae
## 27:                      Clostridiales              Ruminococcaceae
## 28:                      Clostridiales              Lachnospiraceae
## 29:                      Clostridiales              Lachnospiraceae
## 30:                      Clostridiales              Lachnospiraceae
## 31:                      Clostridiales              Lachnospiraceae
## 32:                      Clostridiales              Lachnospiraceae
## 33:                      Clostridiales              Lachnospiraceae
## 34:                      Clostridiales              Lachnospiraceae
## 35:                      Clostridiales              Lachnospiraceae
## 36:                      Clostridiales              Ruminococcaceae
## 37:                      Clostridiales              Ruminococcaceae
## 38:                      Clostridiales              Lachnospiraceae
## 39:                      Clostridiales              Lachnospiraceae
## 40:                    Lactobacillales             Lactobacillaceae
## 41:                    Lactobacillales             Lactobacillaceae
## 42:                      Clostridiales              Ruminococcaceae
## 43:                    Selenomonadales           Acidaminococcaceae
## 44:                    Selenomonadales              Veillonellaceae
## 45:                    Selenomonadales              Veillonellaceae
## 46:                         Bacillales Bacillales_Incertae_Sedis_XI
## 47:                    Selenomonadales              Veillonellaceae
## 48:                    Selenomonadales              Veillonellaceae
## 49:                      Clostridiales             Clostridiaceae_1
## 50:                      Clostridiales             Clostridiaceae_1
## 51:                      Clostridiales              Ruminococcaceae
## 52:                      Clostridiales              Ruminococcaceae
## 53:                      Clostridiales              Ruminococcaceae
## 54:                      Clostridiales              Ruminococcaceae
## 55:                    Lactobacillales             Lactobacillaceae
## 56:                    Lactobacillales             Lactobacillaceae
## 57:                    Lactobacillales             Lactobacillaceae
## 58:                    Lactobacillales              Enterococcaceae
## 59:                    Lactobacillales             Lactobacillaceae
## 60:                    Lactobacillales             Lactobacillaceae
## 61:                    Lactobacillales             Lactobacillaceae
## 62:                    Lactobacillales             Lactobacillaceae
## 63:                  Bifidobacteriales           Bifidobacteriaceae
## 64:                    Burkholderiales               Sutterellaceae
## 65:                    Burkholderiales               Sutterellaceae
## 66:                 Erysipelotrichales          Erysipelotrichaceae
## 67:                 Erysipelotrichales          Erysipelotrichaceae
## 68:                      Clostridiales             Clostridiaceae_1
## 69:                      Clostridiales              Ruminococcaceae
## 70:                      Clostridiales              Lachnospiraceae
## 71:                      Bacteroidales               Bacteroidaceae
## 72:                      Bacteroidales               Bacteroidaceae
## 73:                      Bacteroidales            Marinilabiliaceae
## 74:                      Bacteroidales           Porphyromonadaceae
## 75:                      Bacteroidales           Porphyromonadaceae
## 76:                      Clostridiales              Ruminococcaceae
## 77:                    Actinomycetales               Micrococcaceae
## 78:                    Actinomycetales               Micrococcaceae
## 79:                    Actinomycetales               Micrococcaceae
## 80:                    Selenomonadales              Veillonellaceae
## 81:                    Actinomycetales             Actinomycetaceae
## 82:                    Actinomycetales             Actinomycetaceae
## 83:                    Lactobacillales             Lactobacillaceae
## 84:                      Synergistales               Synergistaceae
## 85: Gammaproteobacteria_incertae_sedis        Candidatus_Carsonella
## 86:                      Clostridiales        Peptostreptococcaceae
## 87:                      Clostridiales        Peptostreptococcaceae
## 88:                 Verrucomicrobiales          Verrucomicrobiaceae
##                                  Order                       Family
##                         Genus           Species    baseMean log2FoldChange
##  1:          Faecalibacterium       prausnitzii   3.0343248    -4.08667447
##  2:          Faecalibacterium       prausnitzii  12.4200116     0.07383313
##  3:                Prevotella                NA   1.4218562    -2.99038716
##  4:            Fructobacillus         fructosus   0.6069870    -1.45628345
##  5:               Leuconostoc                NA   0.7910991    -2.16757269
##  6:             Streptococcus                NA   7.2220258     0.15650568
##  7:               Bacteroides                NA   6.1742670    -5.10177978
##  8:               Bacteroides      massiliensis   1.4127406    -2.95432416
##  9:               Bacteroides                NA   2.1181649    -3.56730011
## 10:               Bacteroides            ovatus   2.0500179     5.87546311
## 11:             Streptococcus                NA 141.8212152    -1.07783869
## 12:               Lactococcus                NA   4.9813725     4.71444079
## 13:                Prevotella             copri  23.6546362    -7.04218661
## 14:                Prevotella                NA   0.1355131    -0.38378361
## 15:                Prevotella                NA   1.2196181    -2.79338036
## 16:                Prevotella                NA   1.5177211    -3.06839238
## 17:                Prevotella                NA   0.5526678    -1.45628345
## 18:                 Bilophila       wadsworthia   0.4065394    -1.32959095
## 19:                        NA                NA   4.7146402    -0.54875931
## 20:      Escherichia/Shigella                NA 884.6984782     9.15519367
## 21:              Burkholderia                NA   1.5174676    -3.04247689
## 22:                Sutterella                NA   0.9485919    -2.43806135
## 23:         Clostridium_XVIII           ramosum   0.2928597     3.08858530
## 24:                  Bacillus                NA   0.6328793    -1.85130097
## 25:           Bifidobacterium                NA   0.9137253     4.69741388
## 26:           Bifidobacterium                NA  29.5647938    -4.19589952
## 27:            Clostridium_IV                NA   0.6908348    -1.88614607
## 28:                 Roseburia                NA   6.3585490    -0.08032018
## 29:          Fusicatenibacter                NA   0.7614378     4.43272462
## 30:          Clostridium_XlVa                NA   1.0507300    -2.53265427
## 31:                     Dorea   formicigenerans   1.0426945    -2.54411530
## 32:          Clostridium_XlVa                NA   0.4065394    -1.32959095
## 33:                        NA                NA   0.3045751     3.09643502
## 34:                        NA                NA   0.3164397    -1.06246727
## 35:                        NA                NA   0.2373297    -0.81386196
## 36:            Flavonifractor           plautii   1.5005720    -3.05642061
## 37:      Pseudoflavonifractor                NA   0.2108480    -0.38378361
## 38:               Coprococcus                NA   1.1064372    -2.61659006
## 39:               Coprococcus                NA   1.2435027    -2.75933626
## 40:             Lactobacillus                NA   0.9137253     4.69741388
## 41:               Pediococcus                NA 245.1927825   -23.83234880
## 42:                        NA                NA   0.3164397    -1.06246727
## 43:           Acidaminococcus                NA   1.2135287     3.63773402
## 44:               Veillonella                NA   1.1866487    -2.74436048
## 45:                 Dialister                NA   2.5541222     0.30398504
## 46:                   Gemella                NA   4.3281375    -4.59513716
## 47:                 Megamonas        funiformis   0.9671687    -2.38760457
## 48:               Megasphaera                NA   0.8702090    -2.30291512
## 49: Clostridium_sensu_stricto     cellulovorans   0.7910991    -2.16757269
## 50: Clostridium_sensu_stricto                NA   0.2052102    -0.75316800
## 51:                        NA                NA   1.8477075     1.97926525
## 52:             Oscillibacter                NA   0.4746595    -1.48540031
## 53:            Clostridium_IV                NA   0.4669911    -1.40253114
## 54:              Ruminococcus                NA   0.9431474     1.68420434
## 55:             Lactobacillus                NA   4.8692199     3.68469522
## 56:             Lactobacillus       delbrueckii   8.7316588     4.35686608
## 57:             Lactobacillus        kalixensis   0.9339822    -2.36063263
## 58:              Enterococcus                NA   0.4065394    -1.32959095
## 59:             Lactobacillus                NA  11.8513219    -6.04952081
## 60:             Lactobacillus                NA   0.6328793    -1.85130097
## 61:             Lactobacillus                NA 183.9223070    -1.69484438
## 62:             Lactobacillus                NA   1.7571582     5.65369332
## 63:                 Scardovia          wiggsiae   0.4930847     2.81586971
## 64:                        NA                NA   0.8130787    -2.22088019
## 65:            Parasutterella excrementihominis   0.4145009    -0.81386196
## 66:              Holdemanella                NA   0.2843712    -0.81386196
## 67:         Clostridium_XVIII                NA   0.5837389    -1.67941216
## 68: Clostridium_sensu_stricto         cadaveris   0.7119892    -2.01813080
## 69:                        NA                NA   0.7004867    -1.93938057
## 70:          Cellulosilyticum       lentocellum   0.3164397    -1.06246727
## 71:               Bacteroides         coprocola   0.4746595    -1.48540031
## 72:               Bacteroides                NA   1.3816696    -2.91458861
## 73:               Anaerophaga                NA   0.1582198    -0.38378361
## 74:               Barnesiella                NA   0.4145009    -0.81386196
## 75:           Parabacteroides            merdae   1.2676146    -2.81318756
## 76:              Ruminococcus                NA   0.6091502     4.10833964
## 77:                    Rothia      mucilaginosa   0.9104805    -2.28159316
## 78:                    Rothia      mucilaginosa   0.2565127    -0.92894597
## 79:                    Rothia      mucilaginosa   2.8571428    -3.99686873
## 80:               Mitsuokella       jalaludinii   0.1582198    -0.38378361
## 81:               Actinomyces     odontolyticus  19.7583316    -6.78109238
## 82:               Actinomyces                NA   3.7733590     2.13611203
## 83:             Lactobacillus           ruminis   0.6325439    -1.80811983
## 84:            Cloacibacillus         evryensis   0.2763339    -0.38378361
## 85:                        NA                NA   0.1582198    -0.38378361
## 86:                Romboutsia                NA   1.1702608    -2.71992544
## 87:           Intestinibacter        bartlettii   0.7119892    -2.01813080
## 88:               Akkermansia       muciniphila   1.6189994    -3.15371731
##                         Genus           Species    baseMean log2FoldChange
##        lfcSE        stat       pvalue         padj Significant
##  1: 3.893324 -1.04966196 2.938736e-01 9.520388e-01       FALSE
##  2: 3.345390  0.02207011 9.823920e-01 9.823920e-01       FALSE
##  3: 3.903272 -0.76612311 4.436031e-01 9.520388e-01       FALSE
##  4: 3.935468 -0.37004075 7.113521e-01 9.520388e-01       FALSE
##  5: 3.917506 -0.55330418 5.800551e-01 9.520388e-01       FALSE
##  6: 3.634720  0.04305852 9.656549e-01 9.823920e-01       FALSE
##  7: 3.324124 -1.53477404 1.248393e-01 9.520388e-01       FALSE
##  8: 3.903743 -0.75679260 4.491741e-01 9.520388e-01       FALSE
##  9: 3.897122 -0.91536789 3.599985e-01 9.520388e-01       FALSE
## 10: 3.695263  1.58999850 1.118351e-01 9.520388e-01       FALSE
## 11: 2.144040 -0.50271379 6.151655e-01 9.520388e-01       FALSE
## 12: 3.658512  1.28862237 1.975294e-01 9.520388e-01       FALSE
## 13: 3.885654 -1.81235542 6.993130e-02 9.520388e-01       FALSE
## 14: 3.949885 -0.09716325 9.225968e-01 9.665299e-01       FALSE
## 15: 3.905993 -0.71515239 4.745149e-01 9.520388e-01       FALSE
## 16: 3.902292 -0.78630513 4.316887e-01 9.520388e-01       FALSE
## 17: 3.935468 -0.37004075 7.113521e-01 9.520388e-01       FALSE
## 18: 3.938388 -0.33759772 7.356664e-01 9.520388e-01       FALSE
## 19: 3.665669 -0.14970238 8.809994e-01 9.665299e-01       FALSE
## 20: 3.358512  2.72596689 6.411343e-03 2.820991e-01       FALSE
## 21: 3.902612 -0.77960013 4.356263e-01 9.520388e-01       FALSE
## 22: 3.911926 -0.62323807 5.331281e-01 9.520388e-01       FALSE
## 23: 3.794537  0.81395569 4.156703e-01 9.520388e-01       FALSE
## 24: 3.925467 -0.47161289 6.372031e-01 9.520388e-01       FALSE
## 25: 3.716779  1.26383987 2.062875e-01 9.520388e-01       FALSE
## 26: 2.927460 -1.43328998 1.517750e-01 9.520388e-01       FALSE
## 27: 3.924505 -0.48060742 6.307955e-01 9.520388e-01       FALSE
## 28: 3.583433 -0.02241431 9.821175e-01 9.823920e-01       FALSE
## 29: 3.724506  1.19015108 2.339870e-01 9.520388e-01       FALSE
## 30: 3.910204 -0.64770384 5.171765e-01 9.520388e-01       FALSE
## 31: 3.910003 -0.65066838 5.152606e-01 9.520388e-01       FALSE
## 32: 3.938388 -0.33759772 7.356664e-01 9.520388e-01       FALSE
## 33: 3.793917  0.81615773 4.144099e-01 9.520388e-01       FALSE
## 34: 3.943331 -0.26943394 7.875958e-01 9.665299e-01       FALSE
## 35: 3.946722 -0.20621211 8.366252e-01 9.665299e-01       FALSE
## 36: 3.902439 -0.78320773 4.335051e-01 9.520388e-01       FALSE
## 37: 3.949885 -0.09716325 9.225968e-01 9.665299e-01       FALSE
## 38: 3.908766 -0.66941586 5.032302e-01 9.520388e-01       FALSE
## 39: 3.906502 -0.70634460 4.799739e-01 9.520388e-01       FALSE
## 40: 3.716779  1.26383987 2.062875e-01 9.520388e-01       FALSE
## 41: 3.884625 -6.13504511 8.513503e-10 7.491883e-08        TRUE
## 42: 3.943331 -0.26943394 7.875958e-01 9.665299e-01       FALSE
## 43: 3.709451  0.98066654 3.267572e-01 9.520388e-01       FALSE
## 44: 3.906729 -0.70247016 4.823860e-01 9.520388e-01       FALSE
## 45: 3.680308  0.08259772 9.341714e-01 9.671422e-01       FALSE
## 46: 3.296026 -1.39414455 1.632740e-01 9.520388e-01       FALSE
## 47: 3.912891 -0.61018938 5.417364e-01 9.520388e-01       FALSE
## 48: 3.914587 -0.58829077 5.563371e-01 9.520388e-01       FALSE
## 49: 3.917506 -0.55330418 5.800551e-01 9.520388e-01       FALSE
## 50: 3.947287 -0.19080652 8.486772e-01 9.665299e-01       FALSE
## 51: 3.676892  0.53829837 5.903711e-01 9.520388e-01       FALSE
## 52: 3.934769 -0.37750633 7.057974e-01 9.520388e-01       FALSE
## 53: 3.936792 -0.35626245 7.216440e-01 9.520388e-01       FALSE
## 54: 3.749966  0.44912519 6.533414e-01 9.520388e-01       FALSE
## 55: 3.641183  1.01194993 3.115620e-01 9.520388e-01       FALSE
## 56: 3.631788  1.19964782 2.302761e-01 9.520388e-01       FALSE
## 57: 3.913420 -0.60321466 5.463659e-01 9.520388e-01       FALSE
## 58: 3.938388 -0.33759772 7.356664e-01 9.520388e-01       FALSE
## 59: 3.886781 -1.55643469 1.196048e-01 9.520388e-01       FALSE
## 60: 3.925467 -0.47161289 6.372031e-01 9.520388e-01       FALSE
## 61: 3.609592 -0.46953905 6.386844e-01 9.520388e-01       FALSE
## 62: 3.698104  1.52880883 1.263118e-01 9.520388e-01       FALSE
## 63: 3.765422  0.74782320 4.545668e-01 9.520388e-01       FALSE
## 64: 3.916324 -0.56708280 5.706579e-01 9.520388e-01       FALSE
## 65: 3.946722 -0.20621211 8.366252e-01 9.665299e-01       FALSE
## 66: 3.946722 -0.20621211 8.366252e-01 9.665299e-01       FALSE
## 67: 3.930146 -0.42731542 6.691496e-01 9.520388e-01       FALSE
## 68: 3.921057 -0.51469052 6.067693e-01 9.520388e-01       FALSE
## 69: 3.923077 -0.49435190 6.210577e-01 9.520388e-01       FALSE
## 70: 3.943331 -0.26943394 7.875958e-01 9.665299e-01       FALSE
## 71: 3.934769 -0.37750633 7.057974e-01 9.520388e-01       FALSE
## 72: 3.904276 -0.74651190 4.553582e-01 9.520388e-01       FALSE
## 73: 3.949885 -0.09716325 9.225968e-01 9.665299e-01       FALSE
## 74: 3.946722 -0.20621211 8.366252e-01 9.665299e-01       FALSE
## 75: 3.905703 -0.72027691 4.713545e-01 9.520388e-01       FALSE
## 76: 3.736091  1.09963595 2.714908e-01 9.520388e-01       FALSE
## 77: 3.915029 -0.58277810 5.600427e-01 9.520388e-01       FALSE
## 78: 3.945106 -0.23546792 8.138456e-01 9.665299e-01       FALSE
## 79: 3.893888 -1.02644678 3.046810e-01 9.520388e-01       FALSE
## 80: 3.949885 -0.09716325 9.225968e-01 9.665299e-01       FALSE
## 81: 3.164536 -2.14283959 3.212598e-02 9.423621e-01       FALSE
## 82: 3.641154  0.58665799 5.574334e-01 9.520388e-01       FALSE
## 83: 3.926692 -0.46046897 6.451796e-01 9.520388e-01       FALSE
## 84: 3.949885 -0.09716325 9.225968e-01 9.665299e-01       FALSE
## 85: 3.949885 -0.09716325 9.225968e-01 9.665299e-01       FALSE
## 86: 3.907105 -0.69614855 4.863358e-01 9.520388e-01       FALSE
## 87: 3.921057 -0.51469052 6.067693e-01 9.520388e-01       FALSE
## 88: 3.901278 -0.80838051 4.188716e-01 9.520388e-01       FALSE
##        lfcSE        stat       pvalue         padj Significant
resdt.dds.d0.broad
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species baseMean
##    1:     Ruminococcaceae                 NA        NA        0
##    2:    Fusobacteriaceae      Fusobacterium nucleatum        0
##    3:    Fusobacteriaceae      Fusobacterium        NA        0
##    4:       Rikenellaceae                 NA        NA        0
##    5:      Eubacteriaceae        Eubacterium        NA        0
##   ---                                                          
## 1586:      Bacteroidaceae        Bacteroides stercoris        0
## 1587:      Bacteroidaceae        Bacteroides        NA        0
## 1588:      Prevotellaceae         Prevotella        NA        0
## 1589:      Prevotellaceae         Prevotella     bivia        0
## 1590: Methanobacteriaceae Methanobrevibacter        NA        0
##       log2FoldChange lfcSE stat pvalue padj Significant
##    1:             NA    NA   NA     NA   NA          NA
##    2:             NA    NA   NA     NA   NA          NA
##    3:             NA    NA   NA     NA   NA          NA
##    4:             NA    NA   NA     NA   NA          NA
##    5:             NA    NA   NA     NA   NA          NA
##   ---                                                  
## 1586:             NA    NA   NA     NA   NA          NA
## 1587:             NA    NA   NA     NA   NA          NA
## 1588:             NA    NA   NA     NA   NA          NA
## 1589:             NA    NA   NA     NA   NA          NA
## 1590:             NA    NA   NA     NA   NA          NA
volcano.d0.broad.shed = ggplot(
  data = resdt.dds.d0.broad[!is.na(Significant)][(pvalue < 1)],
  mapping = aes(x = log2FoldChange,
                y = -log10(pvalue),
                color = Phylum,
                label = OTU, label1 = Genus)) +
  theme_bw() +
  geom_point() + 
  geom_point(data = resdt.dds.d0.broad[(Significant)], size = 7, alpha = 0.7) + 
  # geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
  theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
  geom_hline(yintercept = -log10(alpha)) +
  ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 0 Broad Spectrum Antibiotics ~ Shedding") +
  theme(axis.title = element_text(size=12)) +
  theme(axis.text = element_text(size=12)) +
  theme(legend.text = element_text(size=12)) +
  geom_vline(xintercept = 0, lty = 2)
volcano.d0.broad.shed

summary(res.dds.d0.broad)
## 
## out of 88 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 0, 0% 
## LFC < 0 (down)   : 1, 1.1% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 34, 39% 
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
mcols(res.dds.d0.broad, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
ggplotly(volcano.d0.broad.shed)

Shedding: Day 7 Narrow Spectrum Antibiotics

# Differential Abundance Testing
ds.d7.narrow.shed <- phyloseq_to_deseq2(ps1.d7.narrow, ~Shedding)

geoMeans.ds.d7.narrow.shed <- apply(counts(ds.d7.narrow.shed), 1, gm_mean)
ds.d7.narrow.shed <- estimateSizeFactors(ds.d7.narrow.shed, geoMeans = geoMeans.ds.d7.narrow.shed)

dds.d7.narrow.shed <- DESeq(ds.d7.narrow.shed, test="Wald", fitType="local", betaPrior = FALSE)

alpha = 0.05

# Tabulate and write results
res.dds.d7.narrow.shed = results(dds.d7.narrow.shed, cooksCutoff = FALSE)
sigtab_dds.dds.d7.narrow.shed = res.dds.d7.narrow.shed[which(res.dds.d7.narrow.shed$padj < alpha), ]
sigtab_dds.dds.d7.narrow.shed = cbind(as(sigtab_dds.dds.d7.narrow.shed, "data.frame"), as(tax_table(ps1.d7.narrow)[rownames(sigtab_dds.dds.d7.narrow.shed), ], "matrix"))
summary(res.dds.d7.narrow.shed)
## 
## out of 527 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 107, 20% 
## LFC < 0 (down)   : 17, 3.2% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 394, 75% 
## (mean count < 2)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
head(sigtab_dds.dds.d7.narrow.shed)
##                                                                                                                                                                                                                                            baseMean
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT  317.6602
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 1985.5854
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG   509.0555
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT 1657.9349
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT   789.6057
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT  660.6060
##                                                                                                                                                                                                                                           log2FoldChange
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT     -26.363295
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG      -6.156231
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG       27.726154
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT       8.504610
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT       11.863821
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT      27.880344
##                                                                                                                                                                                                                                              lfcSE
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 3.193587
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 2.186104
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  3.127693
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT 3.063343
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  3.116180
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.127684
##                                                                                                                                                                                                                                                stat
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT -8.255074
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG -2.816075
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG   8.864731
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT  2.776251
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT   3.807168
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT  8.914055
##                                                                                                                                                                                                                                                 pvalue
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 1.518081e-16
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 4.861439e-03
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  7.668889e-19
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT 5.498972e-03
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  1.405671e-04
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 4.919941e-19
##                                                                                                                                                                                                                                                   padj
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 4.675690e-15
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 1.453712e-02
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  1.181009e-16
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT 1.628542e-02
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  4.286601e-04
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 1.181009e-16
##                                                                                                                                                                                                                                            Kingdom
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT Bacteria
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  Bacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Bacteria
##                                                                                                                                                                                                                                                  Phylum
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG    Firmicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG     Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidetes
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT   Fusobacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT    Firmicutes
##                                                                                                                                                                                                                                                   Class
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidia
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG    Clostridia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Negativicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT   Bacteroidia
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  Fusobacteriia
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT    Clostridia
##                                                                                                                                                                                                                                                     Order
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidales
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG   Clostridiales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Selenomonadales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT   Bacteroidales
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  Fusobacteriales
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT   Clostridiales
##                                                                                                                                                                                                                                                     Family
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidaceae
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG  Lachnospiraceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG   Veillonellaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT   Bacteroidaceae
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  Fusobacteriaceae
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT  Ruminococcaceae
##                                                                                                                                                                                                                                                   Genus
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroides
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG       Blautia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG      Dialister
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT   Bacteroides
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT  Fusobacterium
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT  Ruminococcus
##                                                                                                                                                                                                                                           Species
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT    <NA>
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG    <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG     <NA>
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT  ovatus
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT     <NA>
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT    <NA>
write.table(sigtab_dds.dds.d7.narrow.shed, file="./results/deseq_d7_narrow_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file

# Quick check of factor levels
mcols(res.dds.d7.narrow.shed, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
# Prepare to join results data.table and taxonomy table
resdt.dds.d7.narrow.shed = data.table(as(results(dds.d7.narrow.shed, cooksCutoff = FALSE), "data.frame"),
                   keep.rownames = TRUE)
setnames(resdt.dds.d7.narrow.shed, "rn", "OTU")
taxdt.dds.d7.com = data.table(data.frame(as(tax_table(ps1.d7.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d7.com, "rn", "OTU")

# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d7.com, "OTU")
setkeyv(resdt.dds.d7.narrow.shed, "OTU")
resdt.dds.d7.narrow.shed <- taxdt.dds.d7.com[resdt.dds.d7.narrow.shed]
resdt.dds.d7.narrow.shed
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA  0.000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum  2.102246
##    3:    Fusobacteriaceae      Fusobacterium        NA  0.000000
##    4:       Rikenellaceae                 NA        NA  0.000000
##    5:      Eubacteriaceae        Eubacterium        NA  0.000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris  0.000000
## 1587:      Bacteroidaceae        Bacteroides        NA  0.000000
## 1588:      Prevotellaceae         Prevotella        NA 28.552648
## 1589:      Prevotellaceae         Prevotella     bivia  0.000000
## 1590: Methanobacteriaceae Methanobrevibacter        NA  3.401384
##       log2FoldChange    lfcSE     stat       pvalue         padj
##    1:             NA       NA       NA           NA           NA
##    2:       4.948181 3.136987 1.577367 1.147110e-01           NA
##    3:             NA       NA       NA           NA           NA
##    4:             NA       NA       NA           NA           NA
##    5:             NA       NA       NA           NA           NA
##   ---                                                           
## 1586:             NA       NA       NA           NA           NA
## 1587:             NA       NA       NA           NA           NA
## 1588:      23.699942 3.128347 7.575868 3.567343e-14 3.924077e-13
## 1589:             NA       NA       NA           NA           NA
## 1590:       4.134277 3.128144 1.321639 1.862883e-01 2.912528e-01
resdt.dds.d7.narrow.shed[, Significant := padj < alpha]
resdt.dds.d7.narrow.shed[!is.na(Significant)]
##                                                                                                                                                                                                                                             OTU
##   1:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   2:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   3:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGATAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   4:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   5:  ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTATGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##  ---                                                                                                                                                                                                                                           
## 304:  TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATCCCGGGGCTTAACTCCGGAACTGCCTCTAATACTGTTAGACTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 305:  TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCAACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 306:  TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 307:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 308: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##       Kingdom          Phylum            Class              Order
##   1: Bacteria      Firmicutes       Clostridia      Clostridiales
##   2: Bacteria      Firmicutes       Clostridia      Clostridiales
##   3: Bacteria      Firmicutes       Clostridia      Clostridiales
##   4: Bacteria      Firmicutes       Clostridia      Clostridiales
##   5: Bacteria      Firmicutes       Clostridia      Clostridiales
##  ---                                                             
## 304: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 305: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 306: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 307: Bacteria   Bacteroidetes      Bacteroidia      Bacteroidales
## 308:  Archaea   Euryarchaeota  Methanobacteria Methanobacteriales
##                   Family              Genus     Species    baseMean
##   1:     Ruminococcaceae   Faecalibacterium prausnitzii 1295.374899
##   2:     Ruminococcaceae   Faecalibacterium prausnitzii  393.074688
##   3:     Ruminococcaceae   Faecalibacterium          NA    8.445825
##   4:     Ruminococcaceae   Faecalibacterium prausnitzii  134.830487
##   5:     Ruminococcaceae   Faecalibacterium          NA    2.687308
##  ---                                                               
## 304:       Rikenellaceae          Alistipes          NA   12.618977
## 305:       Rikenellaceae          Alistipes  putredinis   12.685397
## 306: Verrucomicrobiaceae        Akkermansia muciniphila 3634.940803
## 307:      Prevotellaceae         Prevotella          NA   28.552648
## 308: Methanobacteriaceae Methanobrevibacter          NA    3.401384
##      log2FoldChange    lfcSE       stat       pvalue         padj
##   1:     -2.7176525 3.060630 -0.8879390 3.745736e-01 5.196786e-01
##   2:      0.3278235 2.629898  0.1246526 9.007986e-01 9.350122e-01
##   3:     21.9907163 3.129995  7.0258003 2.128428e-12 9.932662e-12
##   4:     -1.2160960 3.061475 -0.3972256 6.912011e-01 8.239888e-01
##   5:      5.2969525 3.134988  1.6896244 9.109983e-02 1.670164e-01
##  ---                                                             
## 304:     22.1855474 3.129221  7.0897979 1.343080e-12 7.011334e-12
## 305:     -7.0092234 3.195528 -2.1934478 2.827513e-02 7.507535e-02
## 306:      0.7666401 2.852488  0.2687619 7.881129e-01 8.731404e-01
## 307:     23.6999418 3.128347  7.5758680 3.567343e-14 3.924077e-13
## 308:      4.1342775 3.128144  1.3216393 1.862883e-01 2.912528e-01
##      Significant
##   1:       FALSE
##   2:       FALSE
##   3:        TRUE
##   4:       FALSE
##   5:       FALSE
##  ---            
## 304:        TRUE
## 305:       FALSE
## 306:       FALSE
## 307:        TRUE
## 308:       FALSE
resdt.dds.d7.narrow.shed
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA  0.000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum  2.102246
##    3:    Fusobacteriaceae      Fusobacterium        NA  0.000000
##    4:       Rikenellaceae                 NA        NA  0.000000
##    5:      Eubacteriaceae        Eubacterium        NA  0.000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris  0.000000
## 1587:      Bacteroidaceae        Bacteroides        NA  0.000000
## 1588:      Prevotellaceae         Prevotella        NA 28.552648
## 1589:      Prevotellaceae         Prevotella     bivia  0.000000
## 1590: Methanobacteriaceae Methanobrevibacter        NA  3.401384
##       log2FoldChange    lfcSE     stat       pvalue         padj
##    1:             NA       NA       NA           NA           NA
##    2:       4.948181 3.136987 1.577367 1.147110e-01           NA
##    3:             NA       NA       NA           NA           NA
##    4:             NA       NA       NA           NA           NA
##    5:             NA       NA       NA           NA           NA
##   ---                                                           
## 1586:             NA       NA       NA           NA           NA
## 1587:             NA       NA       NA           NA           NA
## 1588:      23.699942 3.128347 7.575868 3.567343e-14 3.924077e-13
## 1589:             NA       NA       NA           NA           NA
## 1590:       4.134277 3.128144 1.321639 1.862883e-01 2.912528e-01
##       Significant
##    1:          NA
##    2:          NA
##    3:          NA
##    4:          NA
##    5:          NA
##   ---            
## 1586:          NA
## 1587:          NA
## 1588:        TRUE
## 1589:          NA
## 1590:       FALSE
volcano.d7.narrow.shed = ggplot(
  data = resdt.dds.d7.narrow.shed[!is.na(Significant)][(pvalue < 1)],
  mapping = aes(x = log2FoldChange,
                y = -log10(pvalue),
                color = Phylum,
                label = OTU, label1 = Genus)) +
  theme_bw() +
  geom_point() + 
  geom_point(data = resdt.dds.d7.narrow.shed[(Significant)], size = 7, alpha = 0.7) + 
  # geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
  theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
  geom_hline(yintercept = -log10(alpha)) +
  ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 7 Narrow Spectrum Antibiotics ~ Shedding") +
  theme(axis.title = element_text(size=12)) +
  theme(axis.text = element_text(size=12)) +
  theme(legend.text = element_text(size=12)) +
  geom_vline(xintercept = 0, lty = 2)
volcano.d7.narrow.shed

summary(res.dds.d7.narrow.shed)
## 
## out of 527 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 107, 20% 
## LFC < 0 (down)   : 17, 3.2% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 394, 75% 
## (mean count < 2)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
mcols(res.dds.d7.narrow.shed, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
ggplotly(volcano.d7.narrow.shed)

Shedding: Day 7 Broad Spectrum Antibiotics

sample_data(ps1)$day
##   [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
##  [24] -9  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7
##  [47]  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  0  0  0
##  [70]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [93]  0  0  0  0  0  0  0  0
ps1.d7.broad <- subset_samples(ps1.broad, day == "7")
sample_data(ps1.d7.broad)$day
##  [1] 7 7 7 7 7 7 7 7 7 7 7 7 7
## Levels: 7
sample_data(ps1.d7.broad)$randomization_arm
##  [1] Broad spectrum antibiotics Broad spectrum antibiotics
##  [3] Broad spectrum antibiotics Broad spectrum antibiotics
##  [5] Broad spectrum antibiotics Broad spectrum antibiotics
##  [7] Broad spectrum antibiotics Broad spectrum antibiotics
##  [9] Broad spectrum antibiotics Broad spectrum antibiotics
## [11] Broad spectrum antibiotics Broad spectrum antibiotics
## [13] Broad spectrum antibiotics
## Levels: Broad spectrum antibiotics
# Differential Abundance Testing
ds.d7.broad <- phyloseq_to_deseq2(ps1.d7.broad, ~Shedding)

geoMeans.ds.d7.broad <- apply(counts(ds.d7.broad), 1, gm_mean)
ds.d7.broad <- estimateSizeFactors(ds.d7.broad, geoMeans = geoMeans.ds.d7.broad)

dds.d7.broad <- DESeq(ds.d7.broad, test="Wald", fitType="local", betaPrior = FALSE)

alpha = 0.05

# Tabulate and write results
res.dds.d7.broad = results(dds.d7.broad, cooksCutoff = FALSE)
sigtab_dds.dds.d7.broad = res.dds.d7.broad[which(res.dds.d7.broad$padj < alpha), ]
sigtab_dds.dds.d7.broad = cbind(as(sigtab_dds.dds.d7.broad, "data.frame"), as(tax_table(ps1.d7.broad)[rownames(sigtab_dds.dds.d7.broad), ], "matrix"))
summary(res.dds.d7.broad)
## 
## out of 365 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 77, 21% 
## LFC < 0 (down)   : 9, 2.5% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 316, 87% 
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
head(sigtab_dds.dds.d7.broad)
##                                                                                                                                                                                                                                             baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  668.91942
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT  166.40574
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   70.07518
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  709.05959
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG 1577.61624
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG   135.36504
##                                                                                                                                                                                                                                           log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT      27.867029
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT       7.627297
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT       6.621713
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT      27.949214
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG       7.707301
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG        8.600738
##                                                                                                                                                                                                                                              lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.051920
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 2.994864
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 2.784317
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.051917
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG 2.968799
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  3.015846
##                                                                                                                                                                                                                                               stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 9.130984
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 2.546792
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 2.378218
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 9.157921
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG 2.596101
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  2.851849
##                                                                                                                                                                                                                                                 pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 6.787945e-20
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 1.087182e-02
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 1.739652e-02
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5.290672e-20
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG 9.428832e-03
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  4.346570e-03
##                                                                                                                                                                                                                                                   padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5.871573e-18
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 2.748332e-02
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 4.067023e-02
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5.871573e-18
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG 2.434609e-02
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  1.174932e-02
##                                                                                                                                                                                                                                            Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Bacteria
##                                                                                                                                                                                                                                                  Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT    Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG    Firmicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG     Firmicutes
##                                                                                                                                                                                                                                                   Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidia
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT    Clostridia
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidia
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidia
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG    Clostridia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Negativicutes
##                                                                                                                                                                                                                                                     Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidales
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT   Clostridiales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT   Bacteroidales
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT   Bacteroidales
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG   Clostridiales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Selenomonadales
##                                                                                                                                                                                                                                                    Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  Prevotellaceae
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Ruminococcaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT  Bacteroidaceae
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT  Prevotellaceae
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG Lachnospiraceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG  Veillonellaceae
##                                                                                                                                                                                                                                                      Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT       Prevotella
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Faecalibacterium
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT      Bacteroides
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT       Prevotella
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG             <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG         Dialister
##                                                                                                                                                                                                                                               Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT       copri
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT prausnitzii
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT        <NA>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT        <NA>
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG        <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG         <NA>
write.table(sigtab_dds.dds.d7.broad, file="./results/deseq_d7_broad_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file

# Quick check of factor levels
mcols(res.dds.d7.broad, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
# Prepare to join results data.table and taxonomy table
resdt.dds.d7.broad = data.table(as(results(dds.d7.broad, cooksCutoff = FALSE), "data.frame"),
                   keep.rownames = TRUE)
setnames(resdt.dds.d7.broad, "rn", "OTU")
taxdt.dds.d7.com = data.table(data.frame(as(tax_table(ps1.d7.broad), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d7.com, "rn", "OTU")

# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d7.com, "OTU")
setkeyv(resdt.dds.d7.broad, "OTU")
resdt.dds.d7.broad <- taxdt.dds.d7.com[resdt.dds.d7.broad]
resdt.dds.d7.broad
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA 0.0000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum 0.0000000
##    3:    Fusobacteriaceae      Fusobacterium        NA 0.0000000
##    4:       Rikenellaceae                 NA        NA 0.0000000
##    5:      Eubacteriaceae        Eubacterium        NA 0.0000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris 0.0000000
## 1587:      Bacteroidaceae        Bacteroides        NA 0.0000000
## 1588:      Prevotellaceae         Prevotella        NA 0.0000000
## 1589:      Prevotellaceae         Prevotella     bivia 0.0000000
## 1590: Methanobacteriaceae Methanobrevibacter        NA 0.1071357
##       log2FoldChange    lfcSE      stat    pvalue padj
##    1:             NA       NA        NA        NA   NA
##    2:             NA       NA        NA        NA   NA
##    3:             NA       NA        NA        NA   NA
##    4:             NA       NA        NA        NA   NA
##    5:      0.0000000 0.000000 0.0000000 1.0000000   NA
##   ---                                                 
## 1586:             NA       NA        NA        NA   NA
## 1587:             NA       NA        NA        NA   NA
## 1588:             NA       NA        NA        NA   NA
## 1589:             NA       NA        NA        NA   NA
## 1590:      0.9887598 3.145938 0.3142973 0.7532952   NA
resdt.dds.d7.broad[, Significant := padj < alpha]
resdt.dds.d7.broad[!is.na(Significant)]
##                                                                                                                                                                                                                                            OTU
##   1: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   2: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   3: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   4: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCAATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##   5: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##  ---                                                                                                                                                                                                                                          
## 169: GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT
## 170: GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT
## 171:  GCTAGCGTTATCCGGAATTACTGGGCGTAAAGGGTGCGTAGGTGGTTTCTTAAGTCAGAGGTGAAAGGCTACGGCTCAACCGTAGTAAGCCTTTGAAACTGGGAAACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGG
## 172:  GCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGGAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGG
## 173:  GCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTTAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGAGGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTAGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGG
##       Kingdom     Phylum      Class           Order                Family
##   1: Bacteria Firmicutes Clostridia   Clostridiales       Ruminococcaceae
##   2: Bacteria Firmicutes Clostridia   Clostridiales       Ruminococcaceae
##   3: Bacteria Firmicutes Clostridia   Clostridiales       Ruminococcaceae
##   4: Bacteria Firmicutes Clostridia   Clostridiales       Ruminococcaceae
##   5: Bacteria Firmicutes Clostridia   Clostridiales       Ruminococcaceae
##  ---                                                                     
## 169: Bacteria Firmicutes    Bacilli Lactobacillales      Lactobacillaceae
## 170: Bacteria Firmicutes    Bacilli Lactobacillales      Lactobacillaceae
## 171: Bacteria Firmicutes Clostridia   Clostridiales Peptostreptococcaceae
## 172: Bacteria Firmicutes Clostridia   Clostridiales Peptostreptococcaceae
## 173: Bacteria Firmicutes Clostridia   Clostridiales Peptostreptococcaceae
##                 Genus     Species   baseMean log2FoldChange    lfcSE
##   1: Faecalibacterium prausnitzii 166.405736      7.6272967 2.994864
##   2: Faecalibacterium prausnitzii 126.060421      4.1654154 2.758615
##   3: Faecalibacterium prausnitzii   4.048384     -5.4187547 3.112009
##   4: Faecalibacterium          NA   3.464053      5.4671201 3.060913
##   5: Faecalibacterium prausnitzii   8.776203      3.5361118 3.004212
##  ---                                                                
## 169:    Lactobacillus          NA   5.138507     21.0727267 3.058004
## 170:    Lactobacillus          NA   6.321005     21.3597980 3.056868
## 171:       Romboutsia          NA  74.444842      0.3313355 1.713318
## 172:   Clostridium_XI   difficile   5.001132    -20.8649778 3.110211
## 173:  Intestinibacter  bartlettii  36.437630     -0.5115360 1.690242
##            stat       pvalue         padj Significant
##   1:  2.5467919 1.087182e-02 2.748332e-02        TRUE
##   2:  1.5099661 1.310521e-01 2.024286e-01       FALSE
##   3: -1.7412400 8.164151e-02 1.331695e-01       FALSE
##   4:  1.7861075 7.408186e-02 1.281616e-01       FALSE
##   5:  1.1770513 2.391750e-01 3.477082e-01       FALSE
##  ---                                                 
## 169:  6.8910065 5.539901e-12 1.996673e-11        TRUE
## 170:  6.9874783 2.798709e-12 1.075948e-11        TRUE
## 171:  0.1933882 8.466550e-01 9.270336e-01       FALSE
## 172: -6.7085406 1.965805e-11 5.668070e-11        TRUE
## 173: -0.3026407 7.621637e-01 8.561969e-01       FALSE
resdt.dds.d7.broad
##                                                                                                                                                                                                                                              OTU
##    1:  ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
##    2:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
##    3:   ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
##    4:  ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
##    5:  ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
##   ---                                                                                                                                                                                                                                           
## 1586:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587:  TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589:  TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
##        Kingdom        Phylum           Class              Order
##    1: Bacteria    Firmicutes      Clostridia      Clostridiales
##    2: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    3: Bacteria  Fusobacteria   Fusobacteriia    Fusobacteriales
##    4: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
##    5: Bacteria    Firmicutes      Clostridia      Clostridiales
##   ---                                                          
## 1586: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1587: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1588: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1589: Bacteria Bacteroidetes     Bacteroidia      Bacteroidales
## 1590:  Archaea Euryarchaeota Methanobacteria Methanobacteriales
##                    Family              Genus   Species  baseMean
##    1:     Ruminococcaceae                 NA        NA 0.0000000
##    2:    Fusobacteriaceae      Fusobacterium nucleatum 0.0000000
##    3:    Fusobacteriaceae      Fusobacterium        NA 0.0000000
##    4:       Rikenellaceae                 NA        NA 0.0000000
##    5:      Eubacteriaceae        Eubacterium        NA 0.0000000
##   ---                                                           
## 1586:      Bacteroidaceae        Bacteroides stercoris 0.0000000
## 1587:      Bacteroidaceae        Bacteroides        NA 0.0000000
## 1588:      Prevotellaceae         Prevotella        NA 0.0000000
## 1589:      Prevotellaceae         Prevotella     bivia 0.0000000
## 1590: Methanobacteriaceae Methanobrevibacter        NA 0.1071357
##       log2FoldChange    lfcSE      stat    pvalue padj Significant
##    1:             NA       NA        NA        NA   NA          NA
##    2:             NA       NA        NA        NA   NA          NA
##    3:             NA       NA        NA        NA   NA          NA
##    4:             NA       NA        NA        NA   NA          NA
##    5:      0.0000000 0.000000 0.0000000 1.0000000   NA          NA
##   ---                                                             
## 1586:             NA       NA        NA        NA   NA          NA
## 1587:             NA       NA        NA        NA   NA          NA
## 1588:             NA       NA        NA        NA   NA          NA
## 1589:             NA       NA        NA        NA   NA          NA
## 1590:      0.9887598 3.145938 0.3142973 0.7532952   NA          NA
volcano.d7.broad.shed = ggplot(
  data = resdt.dds.d7.broad[!is.na(Significant)][(pvalue < 1)],
  mapping = aes(x = log2FoldChange,
                y = -log10(pvalue),
                color = Phylum,
                label = OTU, label1 = Genus)) +
  theme_bw() +
  geom_point() + 
  geom_point(data = resdt.dds.d7.broad[(Significant)], size = 7, alpha = 0.7) + 
  # geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
  theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
  geom_hline(yintercept = -log10(alpha)) +
  ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 7 Broad Spectrum Antibiotics ~ Shedding") +
  theme(axis.title = element_text(size=12)) +
  theme(axis.text = element_text(size=12)) +
  theme(legend.text = element_text(size=12)) +
  geom_vline(xintercept = 0, lty = 2)
volcano.d7.broad.shed

summary(res.dds.d7.broad)
## 
## out of 365 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)     : 77, 21% 
## LFC < 0 (down)   : 9, 2.5% 
## outliers [1]     : 0, 0% 
## low counts [2]   : 316, 87% 
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
mcols(res.dds.d7.broad, use.names = TRUE)
## DataFrame with 6 rows and 2 columns
##                        type
##                 <character>
## baseMean       intermediate
## log2FoldChange      results
## lfcSE               results
## stat                results
## pvalue              results
## padj                results
##                                                             description
##                                                             <character>
## baseMean                      mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE                  standard error: Shedding Shedding vs No.shedding
## stat                   Wald statistic: Shedding Shedding vs No.shedding
## pvalue              Wald test p-value: Shedding Shedding vs No.shedding
## padj                                               BH adjusted p-values
ggplotly(volcano.d7.broad.shed)
grid.arrange(volcano.d.9.narrow.shed, volcano.d0.narrow.shed, volcano.d7.narrow.shed, volcano.d.9.broad.shed, volcano.d0.broad.shed, volcano.d7.broad.shed, ncol = 3, nrow = 3)

BOOST: Day 7 Narrow vs. Broad

sample_data(ps1)$day
sample_data(ps1)$d7_rota_boost_updated
sample_data(ps1)$randomization_arm
ps1.d7.boost_narrow_v_broad <- ps1 %>%
  subset_samples(
    day == "7" &
    d7_rota_boost_updated == "Yes" &
    randomization_arm != "No antibiotics"
  )
sample_data(ps1.d7.boost_narrow_v_broad)$day
sample_data(ps1.d7.boost_narrow_v_broad)$d7_rota_boost_updated
sample_data(ps1.d7.boost_narrow_v_broad)$randomization_arm

# Differential Abundance Testing
ds.d7.boost_narrow_v_broad <- phyloseq_to_deseq2(ps1.d7.boost_narrow_v_broad, ~randomization_arm)

geoMeans.ds.d7.boost_narrow_v_broad <- apply(counts(ds.d7.boost_narrow_v_broad), 1, gm_mean)
ds.d7.boost_narrow_v_broad <- estimateSizeFactors(ds.d7.boost_narrow_v_broad, geoMeans = geoMeans.ds.d7.boost_narrow_v_broad)

dds.d7.boost_narrow_v_broad <- DESeq(ds.d7.boost_narrow_v_broad, test="Wald", fitType="local", betaPrior = FALSE)

alpha = 0.05

# Tabulate and write results
res.dds.d7.boost_narrow_v_broad = results(dds.d7.boost_narrow_v_broad, cooksCutoff = FALSE)
sigtab_dds.dds.d7.boost_narrow_v_broad = res.dds.d7.boost_narrow_v_broad[which(res.dds.d7.boost_narrow_v_broad$padj < alpha), ]
sigtab_dds.dds.d7.boost_narrow_v_broad = cbind(as(sigtab_dds.dds.d7.boost_narrow_v_broad, "data.frame"), as(tax_table(ps1.d7.boost_narrow_v_broad)[rownames(sigtab_dds.dds.d7.boost_narrow_v_broad), ], "matrix"))
summary(res.dds.d7.boost_narrow_v_broad)
head(sigtab_dds.dds.d7.boost_narrow_v_broad)
write.table(sigtab_dds.dds.d7.boost_narrow_v_broad, file="./results/deseq_d7_boosted_samples.txt", sep = "\t") # Change filename to save results to appropriate file

# Quick check of factor levels
mcols(res.dds.d7.boost_narrow_v_broad, use.names = TRUE)

# Prepare to join results data.table and taxonomy table
resdt.dds.d7.boost_narrow_v_broad = data.table(as(results(dds.d7.boost_narrow_v_broad, cooksCutoff = FALSE), "data.frame"),
                   keep.rownames = TRUE)
setnames(resdt.dds.d7.boost_narrow_v_broad, "rn", "OTU")
taxdt.dds.d0.com = data.table(data.frame(as(tax_table(ps1.d7.boost_narrow_v_broad), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d0.com, "rn", "OTU")

# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d0.com, "OTU")
setkeyv(resdt.dds.d7.boost_narrow_v_broad, "OTU")
resdt.dds.d7.boost_narrow_v_broad <- taxdt.dds.d0.com[resdt.dds.d7.boost_narrow_v_broad]
resdt.dds.d7.boost_narrow_v_broad
resdt.dds.d7.boost_narrow_v_broad[, Significant := padj < alpha]
resdt.dds.d7.boost_narrow_v_broad[!is.na(Significant)]
resdt.dds.d7.boost_narrow_v_broad

volcano.d7.boost_narrow_v_broad_v_treatment = ggplot(
  data = resdt.dds.d7.boost_narrow_v_broad[!is.na(Significant)][(pvalue < 1)],
  mapping = aes(x = log2FoldChange,
                y = -log10(pvalue),
                color = Phylum,
                label = OTU, label1 = Genus)) +
  theme_bw() +
  geom_point() + 
  geom_point(data = resdt.dds.d7.boost_narrow_v_broad[(Significant)], size = 7, alpha = 0.7) + 
  # geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
  theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
  geom_hline(yintercept = -log10(alpha)) +
  ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 7 Boosted ~ Narrow Vs. Broad") +
  theme(axis.title = element_text(size=12)) +
  theme(axis.text = element_text(size=12)) +
  theme(legend.text = element_text(size=12)) +
  geom_vline(xintercept = 0, lty = 2)
volcano.d7.boost_narrow_v_broad_v_treatment
summary(res.dds.d7.boost_narrow_v_broad)
mcols(res.dds.d7.boost_narrow_v_broad, use.names = TRUE)

ggplotly(volcano.d7.boost_narrow_v_broad_v_treatment)